Experiment: 9VHW

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LIJ

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	20% PEG3350, 0.2 M sodium/potassium tartrate tetrahydrate

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.86

Symmetry
Space Group	P 21 21 21

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2021-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.987	SSRF	BL19U1

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.1	50	99.9	0.184	0.992	16	10.3		34440

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18			1.258	0.808	2.1

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.105	44.451	34089	1693	96.389	0.207	0.2062	0.213	0.227	0.2357	39.76

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]
-0.592			-0.08		0.672

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.488
r_dihedral_angle_3_deg	13.617
r_lrange_it	9.752
r_lrange_other	9.74
r_scangle_it	6.893
r_scangle_other	6.892
r_dihedral_angle_2_deg	6.115
r_dihedral_angle_1_deg	5.891
r_mcangle_it	4.586
r_mcangle_other	4.586

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.488
r_dihedral_angle_3_deg	13.617
r_lrange_it	9.752
r_lrange_other	9.74
r_scangle_it	6.893
r_scangle_other	6.892
r_dihedral_angle_2_deg	6.115
r_dihedral_angle_1_deg	5.891
r_mcangle_it	4.586
r_mcangle_other	4.586
r_scbond_it	4.445
r_scbond_other	4.444
r_mcbond_it	3.226
r_mcbond_other	3.217
r_angle_refined_deg	1.559
r_angle_other_deg	0.569
r_symmetry_nbd_refined	0.256
r_nbd_other	0.208
r_symmetry_nbd_other	0.197
r_nbd_refined	0.192
r_xyhbond_nbd_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_other	0.092
r_chiral_restr	0.076
r_symmetry_nbtor_other	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3798
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	4

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.

9VHW | pdb_00009vhw