9U53 | pdb_00009u53

Crystal structure of the CYP154C2 Q230A 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	7CL9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	The reservoir solution contained a final concentration of 0.06 M divalent cations (0.3 M magnesium chloride hexahydrate and 0.3 M calcium chloride dehydrate), 0.1 M Buffer system 2 (1 M sodium HEPES and MOPS, pH 7.5), and 50% (v/v) Precipitant Mix 1 [40% (v/v) PEG 500 MME and 20% (w/v) PEG 20000].

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.505	α = 90
b = 79.353	β = 90
c = 116.995	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	100	PIXEL	DECTRIS PILATUS 6M		2021-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.9785	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.97	50	97.8	0.049	1	28.7	12.3		37350

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	1.97	2			0.832

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	1.97	39.71	35425	1849	97.53	0.18053	0.17779	0.189	0.23439	0.2419	RANDOM	39.54

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		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.762
r_dihedral_angle_4_deg	16.861
r_dihedral_angle_3_deg	13.307
r_long_range_B_refined	7.581
r_long_range_B_other	7.495
r_scangle_other	6.048
r_dihedral_angle_1_deg	5.963
r_mcangle_other	4.148
r_mcangle_it	4.147
r_scbond_it	4.132
r_scbond_other	4.131
r_mcbond_it	3.032
r_mcbond_other	3.029
r_angle_refined_deg	1.586
r_angle_other_deg	1.385
r_chiral_restr	0.073
r_gen_planes_other	0.01
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
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	3012
Nucleic Acid Atoms
Solvent Atoms	387
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	data reduction
MOLREP	phasing