3BEN

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JPZPDB entry 1JPZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP627711% (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 coefficientSolvent content
2.5652.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.82α = 90
b = 148.209β = 98.32
c = 63.792γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2004-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97959APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6535.297.20.04826.14.312582612582617.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6881.70.2494.43.75307

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1JPZ1.6530121940121940382597.240.162140.162140.161220.19125RANDOM18.795
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]
-1.12-0.11-0.621.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.2
r_dihedral_angle_4_deg14.036
r_dihedral_angle_3_deg13.251
r_dihedral_angle_1_deg5.855
r_scangle_it2.752
r_mcangle_it2.095
r_scbond_it1.842
r_angle_refined_deg1.695
r_mcbond_it1.464
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.2
r_dihedral_angle_4_deg14.036
r_dihedral_angle_3_deg13.251
r_dihedral_angle_1_deg5.855
r_scangle_it2.752
r_mcangle_it2.095
r_scbond_it1.842
r_angle_refined_deg1.695
r_mcbond_it1.464
r_nbtor_refined0.312
r_nbd_refined0.212
r_metal_ion_refined0.184
r_symmetry_vdw_refined0.16
r_xyhbond_nbd_refined0.143
r_symmetry_hbond_refined0.131
r_chiral_restr0.124
r_bond_refined_d0.015
r_gen_planes_refined0.007
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 AtomsNumber
Protein Atoms7332
Nucleic Acid Atoms
Solvent Atoms904
Heterogen Atoms153

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing