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Crystal structure of narbomycin-bound cytochrome P450 PikC (CYP107L1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BVJ PDB ENTRY 2BVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 293 0.1 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 coefficient Solvent content 1.9 34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.963 α = 90 b = 64.896 β = 90 c = 92.83 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 110 CCD MARRESEARCH SAGITTAL FOCUSING CRYSTAL AND VERTICAL FOCUSING DOUBLE MIRROR 2005-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-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 1.75 50 97.3 0.06 65.3 11.2 36334 28.6
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 1.75 1.81 80.9 0.37 3.6 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BVJ 1.75 49.77 34218 3408 94.1 0.207 0.207 0.2029 0.232 0.2269 RANDOM 36.1
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] 0.37 7.41 -7.78
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 3.28 c_scbond_it 2.14 c_mcangle_it 1.97 c_angle_deg 1.4 c_improper_angle_d 1.4 c_mcbond_it 1.27 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 3.28 c_scbond_it 2.14 c_mcangle_it 1.97 c_angle_deg 1.4 c_improper_angle_d 1.4 c_mcbond_it 1.27 c_bond_d 0.01 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 Atoms Number Protein Atoms 3051 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 79
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing