4L0F | pdb_00004l0f

Structure of P450sky (CYP163B3), a cytochrome P450 from skyllamycin biosynthesis (open active site)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	0.1 M MES, 12% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.02	α = 90
b = 79.55	β = 104.53
c = 62.88	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	PIXEL	PSI PILATUS 6M		2012-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.978900	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	48.341	98.5	0.08	16.57		36183	35636		-3	25.73

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	94.8		0.367	4.62

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 4LOE	1.9	48.34	35636	33891	1784	100	0.1814	0.1814	0.1793	0.18	0.221	0.22	RANDOM	24.0539

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		-0.16	-1.03		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.657
r_dihedral_angle_4_deg	14.786
r_dihedral_angle_3_deg	12.713
r_dihedral_angle_1_deg	5.274
r_scangle_it	2.76
r_scbond_it	1.747
r_angle_refined_deg	1.258
r_mcangle_it	0.909
r_mcbond_it	0.501
r_chiral_restr	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.657
r_dihedral_angle_4_deg	14.786
r_dihedral_angle_3_deg	12.713
r_dihedral_angle_1_deg	5.274
r_scangle_it	2.76
r_scbond_it	1.747
r_angle_refined_deg	1.258
r_mcangle_it	0.909
r_mcbond_it	0.501
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3403
Nucleic Acid Atoms
Solvent Atoms	418
Heterogen Atoms	109

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
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.