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Crystal structure of peptide-binding domain of Kar2 protein from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OP6 PDB entry 2OP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 0.17 M Ammonium acetate, 0.085 M Sodium citrate, 25.5% PEG 4000, 15% Glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.65 53.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.846 α = 90 b = 103.113 β = 90 c = 80.792 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 315 2008-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
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 1.92 35.1 99.7 0.067 31.919 7 13673 13673 42.9
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 1.92 1.95 98.5 0.806 2 5.5 638
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 2OP6 1.92 35.1 13646 13646 676 99.66 0.188 0.188 0.186 0.1961 0.23 0.2376 RANDOM 27.182
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] -0.36 -0.54 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.389 r_dihedral_angle_4_deg 16.103 r_dihedral_angle_3_deg 15.499 r_dihedral_angle_1_deg 5.634 r_scangle_it 4.339 r_scbond_it 2.475 r_angle_refined_deg 1.581 r_mcangle_it 1.537 r_mcbond_it 0.876 r_angle_other_deg 0.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.389 r_dihedral_angle_4_deg 16.103 r_dihedral_angle_3_deg 15.499 r_dihedral_angle_1_deg 5.634 r_scangle_it 4.339 r_scbond_it 2.475 r_angle_refined_deg 1.581 r_mcangle_it 1.537 r_mcbond_it 0.876 r_angle_other_deg 0.867 r_mcbond_other 0.235 r_chiral_restr 0.097 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1134 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 phasing MOLREP phasing