4UBS | pdb_00004ubs

The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	Sodium chloride, Na/K phosphate, PEG200, 40% tert-butanol

Crystal Properties
Matthews coefficient	Solvent content
4.26	71.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.897	α = 90
b = 139.897	β = 90
c = 65.268	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2013-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.980	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.2	44.4	99.2	32.9	10.8		37612

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	100		4.4	11.1

Refinement

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	2.2	44.4	37259	1860	99.11	0.1794	0.1769	0.19	0.2283	0.24	RANDOM	41.988

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	33.104
r_dihedral_angle_4_deg	22.258
r_dihedral_angle_3_deg	16.398
r_dihedral_angle_1_deg	6.206
r_mcangle_it	4.323
r_mcbond_it	3.414
r_mcbond_other	3.413
r_angle_refined_deg	2.134
r_angle_other_deg	1.09
r_chiral_restr	0.142

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.104
r_dihedral_angle_4_deg	22.258
r_dihedral_angle_3_deg	16.398
r_dihedral_angle_1_deg	6.206
r_mcangle_it	4.323
r_mcbond_it	3.414
r_mcbond_other	3.413
r_angle_refined_deg	2.134
r_angle_other_deg	1.09
r_chiral_restr	0.142
r_bond_refined_d	0.019
r_gen_planes_refined	0.012
r_gen_planes_other	0.012
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3044
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	234

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOLREP	model building
HKL	data reduction

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.