3BEN

Structure of N-(12-imidazolyl-dodecanoyl)-L-leucine inhibitor bound to the heme domain of Cytochrome P450-BM3

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	11% (w/v) PEG-3350, 200 mM magnesium chloride, 7.5% (v/v) glycerol, 100 mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.82	α = 90
b = 148.209	β = 98.32
c = 63.792	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	CCD			2004-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97959	APS	19-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	1.65	35.2	97.2	0.048	26.1	4.3	125826	125826			17.6

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	1.65	1.68	81.7		0.249	4.4	3.7	5307

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 1JPZ	1.65	30	121940	121940	3825	97.24	0.16214	0.16214	0.16122	0.19125	RANDOM	18.795

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]
-1.12		-0.11	-0.62		1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.2
r_dihedral_angle_4_deg	14.036
r_dihedral_angle_3_deg	13.251
r_dihedral_angle_1_deg	5.855
r_scangle_it	2.752
r_mcangle_it	2.095
r_scbond_it	1.842
r_angle_refined_deg	1.695
r_mcbond_it	1.464
r_nbtor_refined	0.312
r_nbd_refined	0.212
r_metal_ion_refined	0.184
r_symmetry_vdw_refined	0.16
r_xyhbond_nbd_refined	0.143
r_symmetry_hbond_refined	0.131
r_chiral_restr	0.124
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7332
Nucleic Acid Atoms
Solvent Atoms	904
Heterogen Atoms	153

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing