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Structure of P450sky (CYP163B3), a cytochrome P450 from skyllamycin biosynthesis (open active site)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LOE PDB ENTRY 4LOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1 M MES, 12% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.35 47.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.02 α = 90 b = 79.55 β = 104.53 c = 62.88 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 PIXEL PSI PILATUS 6M 2012-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.978900 SLS X10SA
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 1.9 48.341 98.5 0.08 16.57 36183 35636 -3 25.73
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 1.9 2 94.8 0.367 4.62
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4LOE 1.9 48.34 35636 33891 1784 100 0.1814 0.1814 0.1793 0.1795 0.221 0.2219 RANDOM 24.0539
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] 0.53 -0.16 -1.03 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.657 r_dihedral_angle_4_deg 14.786 r_dihedral_angle_3_deg 12.713 r_dihedral_angle_1_deg 5.274 r_scangle_it 2.76 r_scbond_it 1.747 r_angle_refined_deg 1.258 r_mcangle_it 0.909 r_mcbond_it 0.501 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.657 r_dihedral_angle_4_deg 14.786 r_dihedral_angle_3_deg 12.713 r_dihedral_angle_1_deg 5.274 r_scangle_it 2.76 r_scbond_it 1.747 r_angle_refined_deg 1.258 r_mcangle_it 0.909 r_mcbond_it 0.501 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3403 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 109
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling