3IW2 | pdb_00003iw2

Crystal structure of Mycobacterium tuberculosis cytochrome P450 CYP125 in complex with econazole

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	Crystallization was refined to two different conditions, both consisting of MgCl2 with 0.1 M HEPES (either pH 7.0 or 7.5) and 20% PEG 6000 or 25% PEG 3350, respectively., VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.632	α = 90
b = 86.016	β = 90
c = 89.455	γ = 90

Symmetry
Space Group	P 21 21 21

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	Bruker Platinum 135	mirrors	2008-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	2.19	50	94.22	0.098	8.7		21805	21805

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.19	2.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 3IVY	2.19	49.63	21805	21805	1179	94.77	0.16497	0.16108	0.17	0.23745	0.25	RANDOM	15.764

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]
-0.08			0.05		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.945
r_dihedral_angle_4_deg	15.704
r_dihedral_angle_3_deg	14.456
r_dihedral_angle_1_deg	8.818
r_scangle_it	5.382
r_scbond_it	3.875
r_mcangle_it	2.195
r_angle_refined_deg	1.866
r_mcbond_it	1.62
r_angle_other_deg	1.237
r_mcbond_other	0.608
r_xyhbond_nbd_other	0.397
r_symmetry_hbond_refined	0.334
r_nbd_refined	0.265
r_xyhbond_nbd_refined	0.229
r_nbd_other	0.215
r_symmetry_vdw_other	0.214
r_nbtor_refined	0.185
r_symmetry_vdw_refined	0.143
r_chiral_restr	0.133
r_nbtor_other	0.092
r_bond_refined_d	0.022
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3126
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing