9M47 | pdb_00009m47

Substrate Promiscuous Cytochrome P450 RufO

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Magnesium Chloride Hexahydrate, 0.1M Tris HCl (pH 8.25), 25% (W/V) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.75	α = 90
b = 76.75	β = 90
c = 135.7	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2021-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7	76.75	99.3	0.94	5.5	6.7		11730

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7				0.945

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.7	76.75	11730	603	99.3	0.232	0.2287	0.2331	0.2824	0.2804	28.14

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]
-1.089			-1.089		2.178

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	20.146
r_dihedral_angle_3_deg	15.054
r_dihedral_angle_6_deg	14.154
r_dihedral_angle_2_deg	7.654
r_dihedral_angle_1_deg	6.975
r_lrange_it	3.864
r_lrange_other	3.864
r_mcangle_it	2.058
r_mcangle_other	2.057
r_scangle_it	1.744
r_scangle_other	1.743
r_angle_refined_deg	1.458
r_mcbond_it	1.162
r_mcbond_other	1.161
r_scbond_it	0.969
r_scbond_other	0.968
r_angle_other_deg	0.508
r_nbd_other	0.221
r_nbd_refined	0.219
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.176
r_symmetry_nbd_refined	0.172
r_xyhbond_nbd_refined	0.153
r_symmetry_xyhbond_nbd_refined	0.136
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.064
r_chiral_restr_other	0.051
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2814
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing