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GID4 fragment in complex with a peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other an unpublished, nearly isomorphous crystal structure of GID4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% PEG3350, 0.2M sodium bromide
Crystal Properties Matthews coefficient Solvent content 2.08 40.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.993 α = 90 b = 40.651 β = 98.39 c = 56.717 γ = 90
Symmetry Space Group P 1 21 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 CCD RIGAKU SATURN A200 2017-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 1.6 40.65 95.4 0.076 0.089 0.046 0.999 13.1 3.7 21138
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 1.6 1.63 90.5 1.351 1.581 0.814 0.424 3.6 1008
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R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT an unpublished, nearly isomorphous crystal structure of GID4 1.6 32.9 20015 1078 95.3 0.2114 0.2095 0.2201 0.2483 0.2565 21.326
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] 0.2 -0.87 -0.77 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_4_deg 23.108 r_dihedral_angle_3_deg 12.272 r_dihedral_angle_1_deg 7.375 r_mcangle_it 2.644 r_mcbond_it 1.689 r_mcbond_other 1.679 r_angle_refined_deg 1.604 r_angle_other_deg 0.962 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_4_deg 23.108 r_dihedral_angle_3_deg 12.272 r_dihedral_angle_1_deg 7.375 r_mcangle_it 2.644 r_mcbond_it 1.689 r_mcbond_other 1.679 r_angle_refined_deg 1.604 r_angle_other_deg 0.962 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1356 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 11
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing