8YHN | pdb_00008yhn

Crystal structure of Cytochrome P450 107P2 from streptomyces avermitilis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		288.15	17.5% PEG 3350, 0.2M Magnesium acetate tetrahydrate, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.128	α = 90
b = 66.44	β = 90
c = 111.756	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	288.15	PIXEL	DECTRIS PILATUS3 6M		2023-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 11C	0.979	PAL/PLS	11C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.986	44.209	99.8	1.88	1.2	12.6		31112

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	1.986	5.1791			0.997

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	THROUGHOUT	1.986	44.209	30653	1466	98.528	0.225	0.2227	0.2294	0.2721	0.2769	37.27

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]
-0.512			-0.98		1.493

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.883
r_dihedral_angle_4_deg	22.968
r_dihedral_angle_3_deg	20.079
r_lrange_it	7.661
r_lrange_other	7.659
r_dihedral_angle_1_deg	5.464
r_scangle_it	4.476
r_scangle_other	4.475
r_mcangle_it	3.928
r_mcangle_other	3.927
r_scbond_it	2.979
r_scbond_other	2.978
r_mcbond_it	2.739
r_mcbond_other	2.735
r_angle_refined_deg	1.463
r_angle_other_deg	1.361
r_symmetry_xyhbond_nbd_refined	0.645
r_nbd_refined	0.221
r_symmetry_nbd_refined	0.205
r_nbd_other	0.202
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.148
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.072
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2985
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing