3KSW | pdb_00003ksw

Crystal structure of sterol 14alpha-demethylase (CYP51) from Trypanosoma cruzi in complex with an inhibitor VNF ((4-(4-chlorophenyl)-N-[2-(1H-imidazol-1-yl)-1-phenylethyl]benzamide)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K1O	PDB entry 3k1o

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	PEG 3350, SODIUM FORMATE, SODIUM CHLORIDE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.468	α = 90
b = 66.468	β = 90
c = 234.281	γ = 120

Symmetry
Space Group	P 31 2 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	MARMOSAIC 225 mm CCD		2006-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.05391	APS	22-BM

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	3.05	50	91.7	0.098	13.1	7.6	13424	12216	2	2

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	3.05	3.1	43.4		0.369	2	2.4	412

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB entry 3k1o	3.05	28.57	2	11544	10505	519	90.96	0.24693	0.24487	0.26	0.29246	0.3	RANDOM	27.778

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]
-0.17	-0.09		-0.17		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.443
r_dihedral_angle_4_deg	15.321
r_dihedral_angle_3_deg	13.504
r_scangle_it	4.265
r_dihedral_angle_1_deg	3.776
r_scbond_it	2.404
r_mcangle_it	1.588
r_mcbond_it	0.82
r_angle_refined_deg	0.62
r_chiral_restr	0.044

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.443
r_dihedral_angle_4_deg	15.321
r_dihedral_angle_3_deg	13.504
r_scangle_it	4.265
r_dihedral_angle_1_deg	3.776
r_scbond_it	2.404
r_mcangle_it	1.588
r_mcbond_it	0.82
r_angle_refined_deg	0.62
r_chiral_restr	0.044
r_gen_planes_refined	0.004
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3514
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	72

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.