9HS4 | pdb_00009hs4

Cytochrome P460 from Methyloccocus capsulatus (double crosslink from Lys)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SFX structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
2	VAPOR DIFFUSION, SITTING DROP	8	293	100 nL protein at 7 mg/mL with 100 nL of precipitant (2.05 M ammonium sulfate, 100 mM Tris-HCl pH 8.0)

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.657	α = 90
b = 80.627	β = 90
c = 84.695	γ = 90

Symmetry
Space Group	P 21 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	293	PIXEL	DECTRIS EIGER2 X 4M		2023-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE VMXi	0.7749	Diamond	VMXi

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.66	58.39	99.72	0.0846	0.999	18.92	80.5		38507

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	1.66	1.719	97.35		0.428		33.7

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	1.66	58.39	36644	1872	99.99	0.14424	0.14224	0.151	0.18324	0.1855	RANDOM	30.178

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]
0.53			-0.72		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.501
r_dihedral_angle_2_deg	13.881
r_long_range_B_refined	9.029
r_long_range_B_other	9.017
r_dihedral_angle_1_deg	6.723
r_scangle_other	6.214
r_scbond_it	4.222
r_scbond_other	4.195
r_mcangle_it	4.092
r_mcangle_other	4.091
r_mcbond_it	3.038
r_mcbond_other	2.999
r_angle_refined_deg	2.211
r_angle_other_deg	0.81
r_chiral_restr	0.13
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2284
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data scaling
DIALS	data reduction
REFMAC	phasing