4Z5Q

Crystal structure of the LnmZ cytochrome P450 hydroxylase from the leinamycin biosynthetic pathway of Streptomyces atroolivaceus S-140 at 1.8 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y98	PDB ENTRY 2Y98

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	0.2 M magnesium chloride, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2	38.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.307	α = 90
b = 83.434	β = 97.67
c = 48.192	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	RAYONIX MX-225	Beryllium Lenses	2013-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.801	46.884	99.7	0.064	0.076	0.041	0.998	12.7	3.4	34256	34256

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	1.801	1.85	98.7		0.838	0.838	1.001	0.541	0.606	1.4	3.3	2524

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2Y98	1.801	46.884	34234	1760	99.68	0.1611	0.159	0.1999	RANDOM	32.207

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]
1.11		0.2	-0.64		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.466
r_dihedral_angle_4_deg	18.379
r_dihedral_angle_3_deg	15.112
r_dihedral_angle_1_deg	6.057
r_mcangle_it	4.449
r_mcbond_it	2.955
r_mcbond_other	2.955
r_angle_refined_deg	1.658
r_angle_other_deg	0.997
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.466
r_dihedral_angle_4_deg	18.379
r_dihedral_angle_3_deg	15.112
r_dihedral_angle_1_deg	6.057
r_mcangle_it	4.449
r_mcbond_it	2.955
r_mcbond_other	2.955
r_angle_refined_deg	1.658
r_angle_other_deg	0.997
r_chiral_restr	0.103
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.008
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2797
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

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.