35WG | pdb_000035wg

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	Prep 2 mM compound in 12% PEG8000, 19% iso-propanol, 0.1 M HEPES pH 7.5, then soaking with the Apo-crystal 1 hr.

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.09

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 PILATUS 6M		2021-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.0	SPring-8	BL45XU

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.97	44.77	98.8	0.108	0.117	0.044	0.998	11.3	6.9		23516

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2.02			0.887	0.957	0.357	0.76	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 (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	1.97	44.77	22338	1176	98.81	0.1661	0.1639	0.1745	0.2068	0.2142	RANDOM	32.772

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]
-1.44		-0.02	-0.14		1.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.982
r_dihedral_angle_4_deg	18.937
r_dihedral_angle_3_deg	13.46
r_dihedral_angle_1_deg	6.759
r_mcangle_it	3.155
r_angle_refined_deg	1.931
r_mcbond_it	1.898
r_mcbond_other	1.896
r_angle_other_deg	1.413
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.982
r_dihedral_angle_4_deg	18.937
r_dihedral_angle_3_deg	13.46
r_dihedral_angle_1_deg	6.759
r_mcangle_it	3.155
r_angle_refined_deg	1.931
r_mcbond_it	1.898
r_mcbond_other	1.896
r_angle_other_deg	1.413
r_chiral_restr	0.098
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2156
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	58

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.