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PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-531-494
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O33 5O33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293.15 0.1M bis-tris pH 5.5 24% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.807 α = 90 b = 62.807 β = 90 c = 342.646 γ = 120
Symmetry Space Group P 65 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 PILATUS 6M 2018-08-02 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.95 85.66 98.4 0.275 0.283 0.066 0.998 8.8 18.4 30148
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 1.95 2.06 99.8 7.137 7.338 1.692 0.433 18.5 4307
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5O33 1.95 57.11 28151 1496 97.19 0.2215 0.2182 0.2311 0.2841 0.2888 RANDOM 45.461
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] 1.4 0.7 1.4 -4.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.709 r_dihedral_angle_4_deg 18.243 r_dihedral_angle_3_deg 15.239 r_dihedral_angle_1_deg 7.528 r_mcangle_it 5.121 r_mcbond_it 3.524 r_mcbond_other 3.523 r_angle_refined_deg 1.524 r_angle_other_deg 1.329 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.709 r_dihedral_angle_4_deg 18.243 r_dihedral_angle_3_deg 15.239 r_dihedral_angle_1_deg 7.528 r_mcangle_it 5.121 r_mcbond_it 3.524 r_mcbond_other 3.523 r_angle_refined_deg 1.524 r_angle_other_deg 1.329 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2773 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing