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Crystal structure of the RhoGAP domain of Rgd1p at 2.19 Angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U3K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.56 298 HEPES, PEG3350, NAN3, TRIS, DTT, PH 7.56
Crystal Properties Matthews coefficient Solvent content 2.24 45.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.23 α = 90 b = 63.23 β = 90 c = 99.73 γ = 120
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 2M-F 2014-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.953700 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim 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 2.19 54.76 99.6 0.041 0.041 0.062 0.99 25.57 13.52 11616 49.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.25 97.9 0.78 0.78 1.06 0.65 2.29 13.28
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 4U3K 2.19 54.76 11067 548 99.63 0.1639 0.162 0.1724 0.2022 0.204 RANDOM 58.73
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] 0.12 0.06 0.12 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.22 r_dihedral_angle_4_deg 18.258 r_dihedral_angle_3_deg 13.392 r_dihedral_angle_1_deg 5.479 r_angle_other_deg 3.697 r_angle_refined_deg 1.469 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_other 0.007 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.22 r_dihedral_angle_4_deg 18.258 r_dihedral_angle_3_deg 13.392 r_dihedral_angle_1_deg 5.479 r_angle_other_deg 3.697 r_angle_refined_deg 1.469 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1601 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing