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The crystal structure of the human RND1 GTPase in the active GTP bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M7B PDB ENTRY 1M7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.2M NAI, 20%(W/V)PEG3350, 0.1M BISTRISPROPANE PH8.5, 10% (V/V) ETHYLENE GLYCOL, 0.5% (V/V) DIMETHYLSULPHOXIDE, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.66 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.168 α = 90 b = 67.762 β = 90 c = 206.409 γ = 90
Symmetry Space Group C 2 2 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 CCD MARRESEARCH 2006-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 2.3 30 95.9 0.06 11 7.7 20279 -3 44.7
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 2.3 2.34 95.5 0.21 7 5
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 PDB ENTRY 1M7B 2.31 30 19213 1021 95.6 0.207 0.205 0.2034 0.236 0.238 RANDOM 30.73
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] 1.25 2.39 -3.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.716 r_dihedral_angle_4_deg 22.426 r_dihedral_angle_3_deg 16.369 r_dihedral_angle_1_deg 6.489 r_scangle_it 2.308 r_angle_refined_deg 1.601 r_scbond_it 1.56 r_angle_other_deg 1.52 r_mcangle_it 1.035 r_mcbond_it 0.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.716 r_dihedral_angle_4_deg 22.426 r_dihedral_angle_3_deg 16.369 r_dihedral_angle_1_deg 6.489 r_scangle_it 2.308 r_angle_refined_deg 1.601 r_scbond_it 1.56 r_angle_other_deg 1.52 r_mcangle_it 1.035 r_mcbond_it 0.609 r_symmetry_vdw_other 0.267 r_symmetry_hbond_refined 0.24 r_nbd_refined 0.202 r_nbd_other 0.196 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.128 r_symmetry_vdw_refined 0.127 r_nbtor_other 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2708 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing