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Crystal Structure of RhoA.GDP.MgF3-in Complex with RhoGAP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 18% PEG2KMME, 100mM MES, 10mM MgCl2, 10mM NaF, 2mM deferoxamine, 114mM (NH4)2SO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.2 43.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.49 α = 90 b = 71.4 β = 90 c = 91.15 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 15 0.083 17.5 5.4 40798 40618 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 99.6 0.401 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1TX4 1.8 15 40618 38536 2038 99.68 0.18774 0.18608 0.1863 0.21893 0.2202 RANDOM 22.779
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] -0.17 1.01 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.152 r_scangle_it 3.313 r_dihedral_angle_1_deg 3.215 r_scbond_it 1.904 r_mcangle_it 1.296 r_angle_refined_deg 1.226 r_mcbond_it 0.669 r_nbd_refined 0.245 r_symmetry_vdw_refined 0.208 r_symmetry_hbond_refined 0.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.152 r_scangle_it 3.313 r_dihedral_angle_1_deg 3.215 r_scbond_it 1.904 r_mcangle_it 1.296 r_angle_refined_deg 1.226 r_mcbond_it 0.669 r_nbd_refined 0.245 r_symmetry_vdw_refined 0.208 r_symmetry_hbond_refined 0.206 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2998 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 33
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement