Experiment: 9VHU

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KU2

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	20% PEG500MME, 10% PEG20000, 0.1 M Buffer System2 pH7.5 (directly mixed by HEPES-Na and MOPS), 0.02 M sodium formate, 0.02 M NH4Ac, 0.02 M sodium citrate, 0.02 M sodium/potassium tartrate, 0.02 M sodium oxamate

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.6

Symmetry
Space Group	P 1 21 1

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		2020-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.987	SSRF	BL18U1

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	3.05	50	100	0.125	0.994	13.99	5.7		50680

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	3.05	3.16			1.025	0.62	1.72

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	3.05	40.2	48950	2472	96.351	0.214	0.213	0.2144	0.241	0.237	83.52

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]
-0.013		-0.169	0.011		0.036

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	17.439
r_lrange_other	17.439
r_dihedral_angle_3_deg	16.395
r_dihedral_angle_6_deg	15.003
r_scangle_it	11.156
r_scangle_other	11.155
r_mcangle_it	11.096
r_mcangle_other	11.096
r_mcbond_it	7.137
r_mcbond_other	7.131

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	17.439
r_lrange_other	17.439
r_dihedral_angle_3_deg	16.395
r_dihedral_angle_6_deg	15.003
r_scangle_it	11.156
r_scangle_other	11.155
r_mcangle_it	11.096
r_mcangle_other	11.096
r_mcbond_it	7.137
r_mcbond_other	7.131
r_scbond_it	6.986
r_scbond_other	6.986
r_dihedral_angle_1_deg	6.336
r_dihedral_angle_2_deg	3.748
r_angle_refined_deg	1.485
r_angle_other_deg	0.517
r_nbd_other	0.23
r_symmetry_nbd_other	0.205
r_symmetry_nbd_refined	0.172
r_nbtor_refined	0.171
r_nbd_refined	0.17
r_xyhbond_nbd_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.162
r_chiral_restr_other	0.111
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.028
r_dihedral_angle_other_2_deg	0.024
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15020
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	184

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.

9VHU | pdb_00009vhu