3CXY | pdb_00003cxy

Crystal structure of the cytochrome P450 CYP121 P346L mutant from M. tuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N40

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	297	2 M ammonium sulphate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.714	α = 90
b = 77.714	β = 90
c = 265.046	γ = 120

Symmetry
Space Group	P 65 2 2

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	ADSC QUANTUM 210		2007-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.96	ESRF	ID14-2

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	1.45	20	100	0.057			78019	78019

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	FOURIER SYNTHESIS	THROUGHOUT	1N40	1.45	25.4	78019	78019	4114	100	0.15408	0.15408	0.15241	0.15	0.18598	0.19	RANDOM	16.583

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]
-0.04	-0.02		-0.04		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.574
r_dihedral_angle_4_deg	15.365
r_dihedral_angle_3_deg	12.199
r_sphericity_free	5.464
r_dihedral_angle_1_deg	5.193
r_scangle_it	3.133
r_sphericity_bonded	2.719
r_scbond_it	2.203
r_angle_other_deg	1.868
r_mcangle_it	1.593
r_angle_refined_deg	1.391
r_mcbond_it	1.172
r_rigid_bond_restr	1.149
r_mcbond_other	0.523
r_symmetry_vdw_refined	0.428
r_symmetry_vdw_other	0.247
r_symmetry_hbond_refined	0.245
r_nbd_refined	0.224
r_nbd_other	0.187
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.174
r_nbtor_other	0.085
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3067
Nucleic Acid Atoms
Solvent Atoms	726
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing