8B2D | pdb_00008b2d

CRYSTAL STRUCTURE OF BACTERIAL FLAVIN CONTAINING MONOOXYGENASE THERMORESISTANT MUTANT, IN COMPLEX WITH NADP+

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XVE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	2M (NH4)SO4, 0.1M Bis-Tris pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.606	α = 90
b = 130.361	β = 90
c = 115.653	γ = 90

Symmetry
Space Group	C 2 2 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	KB focusing mirrors	2020-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979264	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.62	45.27	100	0.065	0.021	0.999	20.7	10.9		120046

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.62	1.65			0.701	0.22	0.898	4.1

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	2XVE	1.62	45.27	113948	6049	99.94	0.1625	0.1616	0.17	0.1797	0.19	RANDOM	21.524

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]
-0.74			0.57		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.506
r_dihedral_angle_4_deg	13.603
r_dihedral_angle_3_deg	12.371
r_dihedral_angle_1_deg	6.83
r_angle_other_deg	1.446
r_angle_refined_deg	1.434
r_chiral_restr	0.08
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.506
r_dihedral_angle_4_deg	13.603
r_dihedral_angle_3_deg	12.371
r_dihedral_angle_1_deg	6.83
r_angle_other_deg	1.446
r_angle_refined_deg	1.434
r_chiral_restr	0.08
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7337
Nucleic Acid Atoms
Solvent Atoms	495
Heterogen Atoms	264

Software

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

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.