☰ Navigation Tabs
PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-565-301
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 2.33 47.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.308 α = 90 b = 62.308 β = 90 c = 340.951 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 2.25 170.48 100 0.297 0.305 0.071 0.998 8.6 18.4 19877
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 2.25 2.39 99.9 4.116 4.226 0.947 0.404 19.6 3096
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 2.25 56.83 18781 971 99.94 0.1949 0.1911 0.2002 0.2702 0.2706 RANDOM 54.901
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] 1.12 0.56 1.12 -3.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.883 r_dihedral_angle_4_deg 15.661 r_dihedral_angle_3_deg 14.192 r_dihedral_angle_1_deg 7.071 r_mcangle_it 5.535 r_mcbond_it 3.636 r_mcbond_other 3.635 r_angle_refined_deg 1.516 r_angle_other_deg 0.994 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.883 r_dihedral_angle_4_deg 15.661 r_dihedral_angle_3_deg 14.192 r_dihedral_angle_1_deg 7.071 r_mcangle_it 5.535 r_mcbond_it 3.636 r_mcbond_other 3.635 r_angle_refined_deg 1.516 r_angle_other_deg 0.994 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 25
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing