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X-ray structure of the substrate-bound cytochrome P450 PimD - a polyene macrolide antibiotic pimaricin epoxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X9P PDB ENTRY 2X9P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 296 0.2 M SODIUM MALONATE, PH 7.0; 20% PEG 3330, T=23 C
Crystal Properties Matthews coefficient Solvent content 2.87 57.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.92 α = 90 b = 99.69 β = 111.92 c = 58.505 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 315 MIRRORS 2009-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 1.95 17.01 99.8 0.07 10 4.1 38650 1.5 30.1
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 1.95 2.06 100 0.52 2.3 4.1
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 2X9P 1.95 67.88 36749 1912 99.78 0.15286 0.14977 0.1509 0.21396 0.2143 RANDOM 30.816
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] 0.89 -0.12 -0.09 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.616 r_dihedral_angle_4_deg 20.808 r_dihedral_angle_3_deg 14.959 r_scangle_it 7.359 r_dihedral_angle_1_deg 5.267 r_scbond_it 5.052 r_mcangle_it 2.975 r_rigid_bond_restr 2.777 r_angle_refined_deg 1.985 r_mcbond_it 1.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.616 r_dihedral_angle_4_deg 20.808 r_dihedral_angle_3_deg 14.959 r_scangle_it 7.359 r_dihedral_angle_1_deg 5.267 r_scbond_it 5.052 r_mcangle_it 2.975 r_rigid_bond_restr 2.777 r_angle_refined_deg 1.985 r_mcbond_it 1.896 r_chiral_restr 0.14 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3006 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing