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Crystal structure of the RhoGAP domain of ARHGAP11A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 291 6% PEG 8000, 0.2M sodium chloride, 0.1M tris, pH 8.0. The protein stock solution was supplemented with 5% Ethylene Glycol,
and 1:100 (m:m) Endoproteinase Glu-C. vapor diffusion, temperature 291K, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.14 42.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.066 α = 90 b = 106.15 β = 97.16 c = 107.335 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 300 mm CCD 2008-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.96863 APS 23-ID-B
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 2.2 50 94.7 0.063 3.4 49354
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) 2.2 2.28 68.7 0.549 1.9 3533
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 1RGP 2.3 20 44569 2233 98.072 0.23 0.227 0.262 0.277 0.3007 thin shells (sftools) 48.527
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] 1.469 -0.986 0.262 -1.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.536 r_dihedral_angle_3_deg 14.962 r_dihedral_angle_4_deg 14.342 r_dihedral_angle_1_deg 5.445 r_scangle_it 1.947 r_mcangle_it 1.903 r_angle_other_deg 1.752 r_scbond_it 1.328 r_angle_refined_deg 1.293 r_mcbond_it 1.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.536 r_dihedral_angle_3_deg 14.962 r_dihedral_angle_4_deg 14.342 r_dihedral_angle_1_deg 5.445 r_scangle_it 1.947 r_mcangle_it 1.903 r_angle_other_deg 1.752 r_scbond_it 1.328 r_angle_refined_deg 1.293 r_mcbond_it 1.226 r_mcbond_other 0.31 r_chiral_restr 0.074 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6461 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling tlsmd refinement FFAS03/SCWRL refinement Coot model building MolProbity model building