7F76 | pdb_00007f76

Crystal Structure of FMN-dependent NADPH-quinone reductase (azoR) from Bacillus cohnii

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	35% 2-propanol, 0.1 M Tris/HCl (pH 8.5)

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.849	α = 90
b = 77.552	β = 90
c = 95.495	γ = 90

Symmetry
Space Group	P 2 21 21

Diffraction

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 S 6M		2018-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.57	50	98.1	0.052	0.055	0.018	28	9.2		45768

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.57	1.71	86.1		0.741	0.821	0.343	2.2	5.3

Refinement

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	3GFR	1.57	47.79	45768	2385	90.14	0.1666	0.1653	0.18	0.1909	0.21	RANDOM	20.541

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]
0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.954
r_dihedral_angle_4_deg	19.018
r_dihedral_angle_3_deg	14.788
r_dihedral_angle_1_deg	6.774
r_angle_refined_deg	1.689
r_angle_other_deg	1.527
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.954
r_dihedral_angle_4_deg	19.018
r_dihedral_angle_3_deg	14.788
r_dihedral_angle_1_deg	6.774
r_angle_refined_deg	1.689
r_angle_other_deg	1.527
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2700
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	94

Software

Software
Software Name	Purpose
XDS	data reduction
XDS	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.