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Crystal structure of YC-17-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 6.5 10% PEG MME 5000,0.1 M MES 6.5, 0.1 M AMMONIUM SULFATE, 0.5 MM DTT 1 MM YC-17, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.21 43.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.088 α = 90 b = 91.972 β = 89.92 c = 68.901 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 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 2.85 50 93.4 0.1 14.1 2.5 17855 75.2
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 2.85 2.95 75.8 0.16 3.8 1.7
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 2.85 32.41 16518 1661 92.5 0.24 0.24 0.2336 0.338 0.3301 RANDOM 23.1
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] 8.69 -9.49 -5.25 -3.44
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 2.19 c_mcangle_it 1.93 c_angle_deg 1.5 c_scbond_it 1.42 c_improper_angle_d 1.32 c_mcbond_it 1.13 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 2.19 c_mcangle_it 1.93 c_angle_deg 1.5 c_scbond_it 1.42 c_improper_angle_d 1.32 c_mcbond_it 1.13 c_bond_d 0.009 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 6056 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 150
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing