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Crystal structure of the RHO GTPASE BINDING DOMAIN of Plexin A4A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R2O PDB entry 2r2o
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 25% PEG3350, 0.2M ammonium acetate, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.93 57.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.79 α = 90 b = 49.79 β = 90 c = 124.25 γ = 90
Symmetry Space Group P 41 21 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 CCD ADSC QUANTUM 315 2012-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97931 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.58 46.217 100 0.052 24.27 22346 -3 28.208
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.62 99.9 0.986 2.18
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2r2o 1.58 46.217 22274 1148 99.973 0.204 0.2029 0.2059 0.2194 0.2149 RANDOM 17.519
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] 0.269 0.269 -0.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.581 r_dihedral_angle_3_deg 10.823 r_dihedral_angle_1_deg 5.23 r_dihedral_angle_4_deg 1.631 r_angle_refined_deg 1.471 r_angle_other_deg 0.944 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.581 r_dihedral_angle_3_deg 10.823 r_dihedral_angle_1_deg 5.23 r_dihedral_angle_4_deg 1.631 r_angle_refined_deg 1.471 r_angle_other_deg 0.944 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 761 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 11
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction