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Structure of a mutant of P450 EryK in complex with erythromycin B.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JJO PDB ENTRY 2JJO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 25% PEG3350, 0.1 M TRIS HCL, PH 8.5, 0.2 M CH3COONH4
Crystal Properties Matthews coefficient Solvent content 1.91 34.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.753 α = 90 b = 36.597 β = 92.93 c = 96.273 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 MARMOSAIC 225 mm CCD 2011-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 30 98.3 0.09 13 3.9 27774 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 2 2.03 77.4 0.44 2.1 3.1
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2JJO 2 29.12 25901 1367 98.15 0.16597 0.16332 0.1668 0.21529 0.2184 RANDOM 17.191
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_4_deg 16.432 r_dihedral_angle_3_deg 14.592 r_dihedral_angle_1_deg 5.149 r_scangle_it 1.981 r_angle_refined_deg 1.41 r_scbond_it 1.397 r_mcangle_it 0.988 r_mcbond_it 0.604 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_4_deg 16.432 r_dihedral_angle_3_deg 14.592 r_dihedral_angle_1_deg 5.149 r_scangle_it 1.981 r_angle_refined_deg 1.41 r_scbond_it 1.397 r_mcangle_it 0.988 r_mcbond_it 0.604 r_nbtor_refined 0.302 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.156 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3030 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing