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Crystal structure of human RAB31 in complex with a GTP analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YVD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 20% isopropanol, 16% PEG 4k, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.64 53.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.769 α = 90 b = 87.769 β = 90 c = 87.769 γ = 90
Symmetry Space Group P 21 3
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 QUANTUM 210 2005-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-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 2.8 30 99.8 0.058 9 5772
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) 2.8 2.9 98.6 0.745 7.6
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB1YVD 2.801 30 5728 260 99.427 0.203 0.1999 0.1961 0.2738 0.2718 74.81
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.927 r_dihedral_angle_3_deg 13.083 r_dihedral_angle_4_deg 9.162 r_dihedral_angle_1_deg 3.722 r_mcangle_it 3.011 r_scangle_it 2.239 r_mcbond_it 1.757 r_scbond_it 1.525 r_angle_refined_deg 1.24 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.927 r_dihedral_angle_3_deg 13.083 r_dihedral_angle_4_deg 9.162 r_dihedral_angle_1_deg 3.722 r_mcangle_it 3.011 r_scangle_it 2.239 r_mcbond_it 1.757 r_scbond_it 1.525 r_angle_refined_deg 1.24 r_nbtor_refined 0.305 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.089 r_metal_ion_refined 0.085 r_chiral_restr 0.081 r_bond_refined_d 0.015 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1265 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 33
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction