☰ Navigation Tabs
Crystal structure of the Ras homolog domain of human GRLF1 (p190RhoGAP)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Native crystal, used for model refinement: 26% PEG 4000, 0.1M Tris-HCl, 0.2M Magnesium chloride, 0.1mM DTT, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K 2 Seleno-methionine derivative crystal, used for MAD phasing: 33% PEG 4000, 0.1M Tris-HCl, 0.2M Magnesium chloride, 0.1mM DTT, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K. A ten-fold excess of GppNHp was added to the protein samples prior to crystallization.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.959 α = 90 b = 108.959 β = 90 c = 51.319 γ = 90
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 2007-11-29 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2007-12-06 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97926 APS 23-ID-B 2 SYNCHROTRON APS BEAMLINE 19-ID 0.97931, 0.97945, 0.98166, 0.97243 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 1,2 1.8 50 95.1 0.075 10.9 6.7 26661
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) 1.8 1.86 61.8 0.456 2.7 1690
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.8 19.26 26626 1352 95.06 0.207 0.205 0.2118 0.247 0.2562 RANDOM 21.063
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] 0.02 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.331 r_dihedral_angle_4_deg 25.159 r_dihedral_angle_3_deg 11.656 r_dihedral_angle_1_deg 6.285 r_scangle_it 3.899 r_mcangle_it 3.601 r_scbond_it 2.861 r_mcbond_it 2.72 r_angle_refined_deg 1.465 r_angle_other_deg 0.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.331 r_dihedral_angle_4_deg 25.159 r_dihedral_angle_3_deg 11.656 r_dihedral_angle_1_deg 6.285 r_scangle_it 3.899 r_mcangle_it 3.601 r_scbond_it 2.861 r_mcbond_it 2.72 r_angle_refined_deg 1.465 r_angle_other_deg 0.954 r_mcbond_other 0.702 r_symmetry_vdw_refined 0.284 r_symmetry_vdw_other 0.229 r_nbd_refined 0.211 r_nbd_other 0.186 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.119 r_chiral_restr 0.086 r_nbtor_other 0.081 r_metal_ion_refined 0.027 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1799 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 39
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MAR345 data collection