2VDN | pdb_00002vdn

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TXV	PDB ENTRY 1TXV

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	11% PEG 3350, 0.7 M MAGNESIUM ACETATE, 0.1 M IMIDAZOLE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.2

Symmetry
Space Group	P 32 2 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC CCD	MIRROR	2003-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	CHESS	A1

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.9	50	100	0.15	14.9	7	50647

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	100	0.62	2.7

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1TXV	2.9	47.19	46249	2421	96.1	0.166	0.163	0.1698	0.213	0.2162	RANDOM	44.6

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.89	0.44	0.89	-1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.968
r_dihedral_angle_4_deg	13.632
r_dihedral_angle_3_deg	11.724
r_dihedral_angle_1_deg	5.174
r_mcangle_it	2.14
r_scangle_it	2.062
r_mcbond_it	1.302
r_scbond_it	1.213
r_angle_refined_deg	0.922
r_angle_other_deg	0.759

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.968
r_dihedral_angle_4_deg	13.632
r_dihedral_angle_3_deg	11.724
r_dihedral_angle_1_deg	5.174
r_mcangle_it	2.14
r_scangle_it	2.062
r_mcbond_it	1.302
r_scbond_it	1.213
r_angle_refined_deg	0.922
r_angle_other_deg	0.759
r_nbd_refined	0.178
r_nbd_other	0.17
r_nbtor_refined	0.17
r_symmetry_vdw_other	0.167
r_symmetry_vdw_refined	0.133
r_xyhbond_nbd_refined	0.128
r_symmetry_hbond_refined	0.128
r_nbtor_other	0.078
r_chiral_restr	0.057
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10342
Nucleic Acid Atoms
Solvent Atoms	364
Heterogen Atoms	205

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

URL: https://www.rcsb.org/experimental/2VDN