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Crystal structure of Saccharomyces cerevisiae OMP synthase in complex with PRP(CH2)P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 0.1 M NaHEPES pH 7.5, 10 % Isopropanol, 20 % PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.48 50.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.56 α = 90 b = 61.56 β = 90 c = 132.49 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 1.73 33.14 97.4 0.058 28.63 13.5 26807 26807
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 1.73 1.77 100 1.45 10.8
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 2PRY 1.73 31 25402 1337 97.4 0.21335 0.21138 0.2212 0.25017 0.2517 RANDOM 37.806
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] 1.68 1.68 -3.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.303 r_dihedral_angle_3_deg 15.734 r_dihedral_angle_4_deg 14.946 r_long_range_B_refined 8.04 r_long_range_B_other 8.013 r_scangle_other 6.401 r_dihedral_angle_1_deg 6.169 r_mcangle_it 5.134 r_mcangle_other 5.132 r_scbond_it 4.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.303 r_dihedral_angle_3_deg 15.734 r_dihedral_angle_4_deg 14.946 r_long_range_B_refined 8.04 r_long_range_B_other 8.013 r_scangle_other 6.401 r_dihedral_angle_1_deg 6.169 r_mcangle_it 5.134 r_mcangle_other 5.132 r_scbond_it 4.275 r_scbond_other 4.25 r_mcbond_it 3.586 r_mcbond_other 3.583 r_angle_refined_deg 1.984 r_angle_other_deg 0.936 r_chiral_restr 0.117 r_bond_refined_d 0.019 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 1668 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Coot model building MOLREP phasing