2C7X

Crystal structure of narbomycin-bound cytochrome P450 PikC (CYP107L1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BVJPDB ENTRY 2BVJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
162930.1 M MES, 6.0 0.8 M AMMONIUM SULFATE, 0.5 MM DTT, 1 MM NARBOMYCIN, T=20 C, pH 6.00
Crystal Properties
Matthews coefficientSolvent content
1.934

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.963α = 90
b = 64.896β = 90
c = 92.83γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHSAGITTAL FOCUSING CRYSTAL AND VERTICAL FOCUSING DOUBLE MIRROR2005-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BMAPS22-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
11.755097.30.0665.311.23633428.6
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)
11.751.8180.90.373.66.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2BVJ1.7549.7734218340894.10.2070.2070.232RANDOM36.1
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]
0.377.41-7.78
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.7
c_scangle_it3.28
c_scbond_it2.14
c_mcangle_it1.97
c_angle_deg1.4
c_improper_angle_d1.4
c_mcbond_it1.27
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.7
c_scangle_it3.28
c_scbond_it2.14
c_mcangle_it1.97
c_angle_deg1.4
c_improper_angle_d1.4
c_mcbond_it1.27
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3051
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms79

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing