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Crystal structure of Saccharomyces cerevisiae OMP synthase in complex with PRP(NH)P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 0.1 M Na HEPES pH 7.5, 10 % isopropanol, 20 % PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.49 50.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.01 α = 90 b = 62.01 β = 90 c = 132.22 γ = 90
Symmetry Space Group P 43 21 2
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 2013-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 33.14 99.3 0.06 28.36 14.2 24622
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 100 1.6 14.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4WML 1.8 29.17 23328 1227 99.31 0.20253 0.20065 0.23763 0.2343 RANDOM 43.653
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] 1.65 1.65 -3.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.911 r_dihedral_angle_3_deg 17.016 r_dihedral_angle_4_deg 11.56 r_long_range_B_refined 8.684 r_long_range_B_other 8.683 r_dihedral_angle_1_deg 6.999 r_scangle_other 6.731 r_mcangle_it 5.997 r_mcangle_other 5.995 r_scbond_it 4.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.911 r_dihedral_angle_3_deg 17.016 r_dihedral_angle_4_deg 11.56 r_long_range_B_refined 8.684 r_long_range_B_other 8.683 r_dihedral_angle_1_deg 6.999 r_scangle_other 6.731 r_mcangle_it 5.997 r_mcangle_other 5.995 r_scbond_it 4.652 r_scbond_other 4.625 r_mcbond_it 4.241 r_mcbond_other 4.24 r_angle_refined_deg 1.979 r_angle_other_deg 0.922 r_chiral_restr 0.123 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1694 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 23
Software Software Software Name Purpose XDS data reduction XSCALE data scaling Coot model building REFMAC refinement MOLREP phasing