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Structure of OxyE (CYP165D3), a Cytochrome P450 Involved in Teicoplanin Biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LFK PDB entry 1LFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1 M Bicine, 0.2 M NaCl, 16% (v/v) polyethylene glycol 20000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.65 53.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.68 α = 90 b = 75.68 β = 90 c = 74.72 γ = 120
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 2010-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97824 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 2.5 50 92.8 0.08 14.8 3.5 16568 16371 3 77.4
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) 2.5 2.6 79.7 0.57 2.7 3.5 1497
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1LFK 2.5 49.27 3 16371 818 100 0.22286 0.22027 0.2148 0.27366 0.2652 RANDOM 85.88
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] -4.22 -2.11 -4.22 6.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.731 r_dihedral_angle_3_deg 17.882 r_dihedral_angle_4_deg 16.563 r_dihedral_angle_1_deg 5.253 r_scangle_it 1.424 r_angle_refined_deg 1.184 r_scbond_it 0.838 r_mcangle_it 0.535 r_mcbond_it 0.282 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.731 r_dihedral_angle_3_deg 17.882 r_dihedral_angle_4_deg 16.563 r_dihedral_angle_1_deg 5.253 r_scangle_it 1.424 r_angle_refined_deg 1.184 r_scbond_it 0.838 r_mcangle_it 0.535 r_mcbond_it 0.282 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2979 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 43
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling