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Crystal structure of Yeast IRC4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 90 mM Sodium nitrate, 90 mM Sodium phosphate dibasic, 90 mM Ammonium sulfate, 0.1 M Sodium HEPES, 0.1 M MOPS, pH 7.5, 12% PEG 550 MME, 6% PEG 20,000
Crystal Properties Matthews coefficient Solvent content 1.96 37.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.57 α = 90 b = 38.69 β = 108.59 c = 67.1 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 100 PIXEL DECTRIS PILATUS 6M-F 2013-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 Diamond I04
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 1.61 63.6 97.92 0.071 9.8 4.2 45428
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 1.61 1.65 98.6 0.576 2.1 4.3 3315
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 FREE R-VALUE 5CIV 1.613 63.599 1.91 45428 2290 97.92 0.1939 0.1917 0.1942 0.2358 0.2366
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 12.089 f_angle_d 0.972 f_chiral_restr 0.038 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2851 Nucleic Acid Atoms Solvent Atoms 653 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement PHENIX phasing xia2 data scaling xia2 data reduction