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Fragment of GID4 in complex with a short peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CCR early version of model from PDB entry 6CCR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% PEG3350, 2% Tacsimate pH 7.0 and 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.05 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.14 α = 90 b = 40.14 β = 90 c = 203.343 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS EIGER X 16M 2017-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.1 101.67 100 0.051 0.053 0.016 0.999 22.4 11.8 10614
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 100 1.05 1.102 0.326 0.921 11 827
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT early version of model from PDB entry 6CCR 2.4 39.3 6457 717 99.94 0.2219 0.2177 0.2174 0.2596 0.2647 60.158
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.358 r_dihedral_angle_3_deg 13.597 r_dihedral_angle_4_deg 8.484 r_dihedral_angle_1_deg 7.296 r_mcangle_it 2.977 r_mcbond_it 1.917 r_mcbond_other 1.915 r_angle_refined_deg 1.638 r_angle_other_deg 0.984 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.358 r_dihedral_angle_3_deg 13.597 r_dihedral_angle_4_deg 8.484 r_dihedral_angle_1_deg 7.296 r_mcangle_it 2.977 r_mcbond_it 1.917 r_mcbond_other 1.915 r_angle_refined_deg 1.638 r_angle_other_deg 0.984 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1270 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction PHASER phasing