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Crystal structure of the nucleotide-binding domain of Ras-related GTP-binding protein C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q3F PDB entry 2Q3F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 2.0M ammonium sulfate, 0.2M sodium chloride, 0.1M HEPES. 1:100 (w/w) papain and GMPPNP were also added. Please note: mass spectral analysis of TEV protease digest prior to crystallization suggested that removal of the His-tag was incomplete even after 2 days. However, without TEV protease treatment no crystals were obtained using otherwise identical crystallization conditions. Also note the presence of papain in the crystallization drop., pH 7.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.06 40.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.22 α = 90 b = 72.22 β = 90 c = 72.182 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 ADSC Q315 2009-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 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 1.4 25 100 0.055 12.5 7.3 36466
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) 1.4 1.42 100 0.816 7.2 1835
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 2Q3F 1.4 22.84 36436 1811 99.956 0.155 0.154 0.1649 0.181 0.1872 RANDOM 14.63
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] -0.282 -0.282 0.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.24 r_dihedral_angle_3_deg 11.149 r_dihedral_angle_4_deg 7.143 r_dihedral_angle_1_deg 5.517 r_scangle_it 4.536 r_scbond_it 3.197 r_mcangle_it 1.918 r_angle_refined_deg 1.515 r_mcbond_it 1.263 r_rigid_bond_restr 1.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.24 r_dihedral_angle_3_deg 11.149 r_dihedral_angle_4_deg 7.143 r_dihedral_angle_1_deg 5.517 r_scangle_it 4.536 r_scbond_it 3.197 r_mcangle_it 1.918 r_angle_refined_deg 1.515 r_mcbond_it 1.263 r_rigid_bond_restr 1.169 r_angle_other_deg 0.941 r_mcbond_other 0.407 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1516 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 42
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling