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Crystal structure of human RAB9B in complex with a GTP analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WMS pdb entry 1wms
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 2M ammonium sulfate, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.5 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.43 α = 90 b = 70.43 β = 90 c = 97.715 γ = 120
Symmetry Space Group P 32 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 2006-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 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 2.2 30 99.9 0.107 10.2 6.1 14718
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) 2.2 2.28 100 0.725 5.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT pdb entry 1wms 2.2 23.051 14665 738 99.83 0.215 0.2135 0.2233 0.2531 0.2549 random 31.515
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] 2.436 1.218 2.436 -3.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.515 r_dihedral_angle_3_deg 13.579 r_dihedral_angle_4_deg 11.395 r_dihedral_angle_1_deg 6.076 r_mcangle_it 3.792 r_scangle_it 3.185 r_mcbond_it 2.729 r_scbond_it 2.399 r_angle_refined_deg 1.416 r_angle_other_deg 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.515 r_dihedral_angle_3_deg 13.579 r_dihedral_angle_4_deg 11.395 r_dihedral_angle_1_deg 6.076 r_mcangle_it 3.792 r_scangle_it 3.185 r_mcbond_it 2.729 r_scbond_it 2.399 r_angle_refined_deg 1.416 r_angle_other_deg 0.95 r_mcbond_other 0.701 r_symmetry_vdw_other 0.213 r_nbd_other 0.196 r_nbd_refined 0.182 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.166 r_symmetry_vdw_refined 0.12 r_nbtor_other 0.084 r_chiral_restr 0.076 r_bond_refined_d 0.017 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 1368 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 40
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