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Crystal structure of human RAB4B in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BME pdb entry 2bme
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 18% PEG8000, 0.2M magnesium acetate, 0.1M sodium cacodylate, pH 6.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.295 46.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.528 α = 90 b = 67.528 β = 90 c = 179.955 γ = 90
Symmetry Space Group P 43 21 2
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 2006-10-25 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 30 100 0.119 9 6.2 40474
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 0.976 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT pdb entry 2bme 2.2 20 21799 1033 99.177 0.216 0.2135 0.2165 0.2693 0.2586 thin shells 33.089
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] 1.466 1.466 -2.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.851 r_dihedral_angle_4_deg 19.032 r_dihedral_angle_3_deg 15.358 r_dihedral_angle_1_deg 6.431 r_mcangle_it 3.663 r_scangle_it 3.256 r_mcbond_it 2.456 r_scbond_it 2.394 r_angle_refined_deg 1.409 r_angle_other_deg 0.907
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.851 r_dihedral_angle_4_deg 19.032 r_dihedral_angle_3_deg 15.358 r_dihedral_angle_1_deg 6.431 r_mcangle_it 3.663 r_scangle_it 3.256 r_mcbond_it 2.456 r_scbond_it 2.394 r_angle_refined_deg 1.409 r_angle_other_deg 0.907 r_mcbond_other 0.653 r_symmetry_vdw_other 0.299 r_nbd_refined 0.198 r_nbd_other 0.193 r_symmetry_hbond_refined 0.179 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.147 r_symmetry_vdw_refined 0.117 r_nbtor_other 0.087 r_chiral_restr 0.079 r_bond_refined_d 0.016 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2538 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 63
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