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Crystal structure of CRYI-B Rac1 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GZL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 279 8% v/v PEG4,000
0.1M Tris pH 8.5
0.2M Sodium acetate
Crystal Properties Matthews coefficient Solvent content 3.37 63.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.87 α = 90 b = 81.87 β = 90 c = 355.87 γ = 120
Symmetry Space Group P 62 2 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 2020-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97624 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.1 59.382 97.92 0.99 18.7 10.6 13493
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.21 0.917
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4GZL 3.1 59.382 13493 672 97.839 0.25 0.2486 0.2505 0.2818 0.2882 79.88
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] 0.897 0.449 0.897 -2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.659 r_dihedral_angle_4_deg 17.705 r_dihedral_angle_3_deg 17.265 r_lrange_it 14.802 r_lrange_other 14.801 r_scangle_it 11.188 r_scangle_other 11.186 r_mcangle_other 10.795 r_mcangle_it 10.794 r_scbond_it 7.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.659 r_dihedral_angle_4_deg 17.705 r_dihedral_angle_3_deg 17.265 r_lrange_it 14.802 r_lrange_other 14.801 r_scangle_it 11.188 r_scangle_other 11.186 r_mcangle_other 10.795 r_mcangle_it 10.794 r_scbond_it 7.44 r_scbond_other 7.438 r_mcbond_other 7.399 r_mcbond_it 7.398 r_dihedral_angle_1_deg 4.273 r_angle_other_deg 1.128 r_angle_refined_deg 1.087 r_symmetry_nbd_refined 0.499 r_chiral_restr_other 0.395 r_symmetry_xyhbond_nbd_refined 0.277 r_nbd_other 0.275 r_symmetry_nbd_other 0.228 r_nbd_refined 0.209 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.157 r_symmetry_nbtor_other 0.081 r_metal_ion_refined 0.067 r_chiral_restr 0.042 r_symmetry_xyhbond_nbd_other 0.022 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3567 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling MOLREP phasing