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Crystal structure of RhoGDI K(199,200)R double mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KMT PDB ENTRY 1KMT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 30% PEG 400, 0.1 M Tris, 0.2 M lithium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP,
temperature 294.0K
Crystal Properties Matthews coefficient Solvent content 2.19 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.66 α = 90 b = 58.24 β = 92.49 c = 75.05 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD CUSTOM-MADE monochromator , mirrors 2002-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9190 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 1.6 30 99.6 0.053 15.2 3.7 84662 -3 22
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) 1.6 1.66 99.4 0.382 2.7 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1KMT 1.6 27.02 1 82684 1676 100 0.17281 0.17202 0.1826 0.20998 0.2195 RANDOM 16.983
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] 0.05 -0.02 -0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.286 r_dihedral_angle_1_deg 6.864 r_scangle_it 4.753 r_sphericity_free 4.3 r_scbond_it 3.097 r_sphericity_bonded 2.369 r_mcangle_it 2.267 r_angle_refined_deg 1.719 r_rigid_bond_restr 1.711 r_mcbond_it 1.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.286 r_dihedral_angle_1_deg 6.864 r_scangle_it 4.753 r_sphericity_free 4.3 r_scbond_it 3.097 r_sphericity_bonded 2.369 r_mcangle_it 2.267 r_angle_refined_deg 1.719 r_rigid_bond_restr 1.711 r_mcbond_it 1.362 r_angle_other_deg 0.895 r_symmetry_vdw_other 0.316 r_nbd_other 0.259 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.174 r_symmetry_vdw_refined 0.124 r_chiral_restr 0.119 r_nbtor_other 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4472 Nucleic Acid Atoms Solvent Atoms 779 Heterogen Atoms 40
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing REFMAC refinement HKL-2000 data reduction