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Crystal structure of the LnmA cytochrome P450 hydroxylase from the leinamycin biosynthetic pathway of Streptomyces atroolivaceus S-140 at 1.9 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.77 298 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 6.77, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.2 44.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.759 α = 90 b = 75.454 β = 98.91 c = 93.858 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 ADSC QUANTUM 315r mirrors 2014-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 46.36 94.9 0.092 0.108 0.056 0.997 11.1 3.7 57513 57513
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 70.1 0.833 0.833 0.991 0.53 0.733 1.6 3.2 3115
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 4Z5Q 1.9 46.36 57510 2884 94.73 0.1922 0.1908 0.199 0.2167 0.2257 RANDOM 34.8009
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] 0.8 0.6 -0.23 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.174 r_dihedral_angle_4_deg 15.402 r_dihedral_angle_3_deg 13.099 r_dihedral_angle_1_deg 5.525 r_mcangle_it 3.298 r_mcbond_it 2.195 r_mcbond_other 2.194 r_angle_refined_deg 1.49 r_angle_other_deg 1.083 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.174 r_dihedral_angle_4_deg 15.402 r_dihedral_angle_3_deg 13.099 r_dihedral_angle_1_deg 5.525 r_mcangle_it 3.298 r_mcbond_it 2.195 r_mcbond_other 2.194 r_angle_refined_deg 1.49 r_angle_other_deg 1.083 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6005 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 96
Software Software Software Name Purpose XDS data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection XDS data scaling