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Crystal structure of human Rab3B GTPase bound with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GF9 PDB ENTRY 2GF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 2M ammonium sulfate, 0.2M sodium acetate, 0.1M HEPES, 5% MPD, pH 7.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.4 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.969 α = 90 b = 50.875 β = 110.91 c = 73.553 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 100 IMAGE PLATE RIGAKU RAXIS 2008-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5418
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 1.9 25 99.7 0.061 6.7 15627
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 1.9 1.97 97.9 0.609 3.3 1500
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 2GF9 1.9 20 15562 763 99.724 0.213 0.211 0.2441 0.251 0.2798 RANDOM 15.646
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] -1.208 -1.59 1.537 -1.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.192 r_dihedral_angle_4_deg 16.515 r_dihedral_angle_3_deg 12.066 r_dihedral_angle_1_deg 6.644 r_scangle_it 2.368 r_mcangle_it 2.134 r_scbond_it 1.684 r_mcbond_it 1.403 r_angle_refined_deg 1.381 r_angle_other_deg 0.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.192 r_dihedral_angle_4_deg 16.515 r_dihedral_angle_3_deg 12.066 r_dihedral_angle_1_deg 6.644 r_scangle_it 2.368 r_mcangle_it 2.134 r_scbond_it 1.684 r_mcbond_it 1.403 r_angle_refined_deg 1.381 r_angle_other_deg 0.862 r_mcbond_other 0.415 r_chiral_restr 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1390 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ARP/wARP model building Coot model building MolProbity model building