4Z5P | pdb_00004z5p

Crystal structure of the LnmA cytochrome P450 hydroxylase from the leinamycin biosynthetic pathway of Streptomyces atroolivaceus S-140 at 1.9 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Z5Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.77	298	0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 6.77, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.759	α = 90
b = 75.454	β = 98.91
c = 93.858	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r	mirrors	2014-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	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	1.9	46.36	94.9	0.092	0.108	0.056	0.997	11.1	3.7	57513	57513

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95	70.1		0.833	0.833	0.991	0.53	0.733	1.6	3.2	3115

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	4Z5Q	1.9	46.36	57510	2884	94.73	0.1922	0.1908	0.2	0.2167	0.23	RANDOM	34.8009

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]
0.8		0.6	-0.23		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.174
r_dihedral_angle_4_deg	15.402
r_dihedral_angle_3_deg	13.099
r_dihedral_angle_1_deg	5.525
r_mcangle_it	3.298
r_mcbond_it	2.195
r_mcbond_other	2.194
r_angle_refined_deg	1.49
r_angle_other_deg	1.083
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.174
r_dihedral_angle_4_deg	15.402
r_dihedral_angle_3_deg	13.099
r_dihedral_angle_1_deg	5.525
r_mcangle_it	3.298
r_mcbond_it	2.195
r_mcbond_other	2.194
r_angle_refined_deg	1.49
r_angle_other_deg	1.083
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6005
Nucleic Acid Atoms
Solvent Atoms	379
Heterogen Atoms	96

Software

Software
Software Name	Purpose
XDS	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
XDS	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.