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Crystal structure of Saccharomyces cerevisiae Mep2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B2J PDB ENTRY 2B2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1 M MES PH 6.0, 0.2 M AMMONIUM PHOSPHATE DIBASIC 30% PEG400
Crystal Properties Matthews coefficient Solvent content 3.5 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.692 α = 90 b = 232.35 β = 90 c = 279.189 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 3.2 49 99.9 0.09 9.6 4.2 111848 -3 90.77
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 3.2 3.25 100 0.92 2 4.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2B2J 3.2 49.276 1.33 111734 2451 99.82 0.1905 0.1894 0.1989 0.2409 0.2519 72.55
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.308 f_angle_d 1.154 f_chiral_restr 0.051 f_bond_d 0.012 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 30531 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing