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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 7.5 20% PEG 3350, 0.2 M MGCL2, 0.5 MM DTT, 1 MM YC-17, pH 7.50
Crystal Properties Matthews coefficient Solvent content 1.93 35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.401 α = 90 b = 92.102 β = 89.99 c = 67.574 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 110 CCD MARRESEARCH MIRRORS 2005-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 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 1.7 50 99.4 0.08 22.9 3.8 78149 19.8
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 1.7 1.76 99.7 0.42 2.8 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1.7 39.84 2 71229 7136 90.6 0.29 0.29 0.293 0.333 0.3347 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] -0.2 -4.13 4.33
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.8 c_scangle_it 2.35 c_scbond_it 1.92 c_mcangle_it 1.86 c_mcbond_it 1.34 c_angle_deg 1.3 c_improper_angle_d 1.1 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.8 c_scangle_it 2.35 c_scbond_it 1.92 c_mcangle_it 1.86 c_mcbond_it 1.34 c_angle_deg 1.3 c_improper_angle_d 1.1 c_bond_d 0.008 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 6051 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 150
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing