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Complex between a GID4 fragment and 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 and 0.03M Citric acid
Crystal Properties Matthews coefficient Solvent content 2.18 37.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.045 α = 90 b = 43.669 β = 90 c = 99.984 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 PILATUS3 6M 2017-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97945 APS 19-ID
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 1.7 43.67 99.9 0.071 0.078 0.031 0.999 14.7 6.4 20007
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 1.7 1.73 99.2 1.788 1.942 0.751 0.671 6.5 1044
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 1.75 40 17417 908 99.89 0.193 0.1909 0.2002 0.2359 0.2423 31.715
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] -1.52 2.02 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.693 r_dihedral_angle_4_deg 22.921 r_dihedral_angle_3_deg 13.431 r_dihedral_angle_1_deg 7.06 r_mcangle_it 1.673 r_angle_refined_deg 1.65 r_mcbond_it 1.057 r_mcbond_other 1.057 r_angle_other_deg 0.946 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.693 r_dihedral_angle_4_deg 22.921 r_dihedral_angle_3_deg 13.431 r_dihedral_angle_1_deg 7.06 r_mcangle_it 1.673 r_angle_refined_deg 1.65 r_mcbond_it 1.057 r_mcbond_other 1.057 r_angle_other_deg 0.946 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1359 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing