Experiment: 8A8L

Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a heme-coordinated fragment

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PQ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277.15	0.1M Bis-Tris propane pH 8.5, 0.2M Ammonium nitrate, 18% v/v PEG Smear High

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.77	α = 90
b = 108.169	β = 90
c = 105.25	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 EIGER X 16M		2020-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.88	55.13	100	0.113	0.033	0.999	13.1	12.8		37815			30.86

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	1.88	1.92	100		1.955	0.583	0.866	1.5	12.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7PQ1	1.88	48.1	1.34	37418	1884	98.98	0.2001	0.198	0.1969	0.2357	0.2347	49.19

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.8387
f_angle_d	1.0746
f_chiral_restr	0.0613
f_bond_d	0.0138
f_plane_restr	0.0101

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3177
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	76

Software

Software
Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing