3TIK | pdb_00003tik

Sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei in complex with the tipifarnib derivative 6-((4-chlorophenyl)(methoxy)(1-methyl-1H-imidazol-5-yl)methyl)-4-(2,6-difluorophenyl)-1-methylquinolin-2(1H)-one

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3G1Q	PDB entry 3g1q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.4	297	POTASSIUM PHOSPHATE, SODIUM CHLORIDE, GLYCEROL, PEG 5000, n-TETRADECYL-BETA-D-MALTOSIDE, 6-((4-CHLOROPHENYL)(METHOXY)(1-METHYL-1H-IMIDAZOL-YL)METHYL)-4-(2,6-DIFLUOROPHENYL)-1-METHYLQUINOLIN-2(1H)-ONE, pH 7.4, VAPOR DIFFUSION, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.722	α = 74.47
b = 79.715	β = 81.58
c = 117.521	γ = 68.05

Symmetry
Space Group	P 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	Be Lenses/Diamond Laue Mono	2011-08-07	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 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	2.05	50	94	0.049	43.6	6	122058	115222	2.8	2.8	38.7

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	2.05	2.09	95.4		0.695	2.8	5.9	8174

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 3g1q	2.05	30	122058	115222	6082	99.39	0.18887	0.18887	0.18593	0.19	0.24338	0.24	RANDOM	49.848

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]
0.88	-0.23	0.9	-1.21	-0.65	0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.132
r_dihedral_angle_4_deg	19.828
r_dihedral_angle_3_deg	17.457
r_scangle_it	7.841
r_dihedral_angle_1_deg	6.315
r_scbond_it	5.147
r_mcangle_it	3.311
r_rigid_bond_restr	2.838
r_mcbond_it	1.963
r_angle_refined_deg	1.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.132
r_dihedral_angle_4_deg	19.828
r_dihedral_angle_3_deg	17.457
r_scangle_it	7.841
r_dihedral_angle_1_deg	6.315
r_scbond_it	5.147
r_mcangle_it	3.311
r_rigid_bond_restr	2.838
r_mcbond_it	1.963
r_angle_refined_deg	1.135
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14300
Nucleic Acid Atoms
Solvent Atoms	295
Heterogen Atoms	316

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.