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PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-004-412-710
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 2.34 47.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.49 α = 90 b = 62.49 β = 90 c = 341.271 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 2018-08-03 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 2.26 54.12 99.2 0.137 0.143 0.039 0.998 10.9 10.7 19514
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 2.26 2.39 98.1 1.575 1.663 0.494 0.417 8.6 2696
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5O33 2.26 56.88 18445 949 98.94 0.2012 0.1977 0.2699 0.2483 RANDOM 52.975
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] 0.85 0.43 0.85 -2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.058 r_dihedral_angle_4_deg 20.423 r_dihedral_angle_3_deg 14.165 r_dihedral_angle_1_deg 6.815 r_mcangle_it 5.856 r_mcbond_it 3.756 r_mcbond_other 3.754 r_angle_refined_deg 1.57 r_angle_other_deg 1.007 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.058 r_dihedral_angle_4_deg 20.423 r_dihedral_angle_3_deg 14.165 r_dihedral_angle_1_deg 6.815 r_mcangle_it 5.856 r_mcbond_it 3.756 r_mcbond_other 3.754 r_angle_refined_deg 1.57 r_angle_other_deg 1.007 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2773 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing