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Crystal structure of human RAB5B in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N6I PDB ENTRY 1N6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 291 25% P3350, 0.1M NaOAc, pH 4.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.1 37.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.302 α = 90 b = 78.37 β = 90 c = 95.501 γ = 90
Symmetry Space Group P 21 21 21
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 4 2006-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 CHESS F1
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 1.5 50 100 0.058 9.2 7 50161
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) 1.5 1.55 100 0.679 6.7
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 1N6I 1.55 30 45443 2875 99.184 0.264 0.2622 0.2662 0.2936 0.296 thin shells 15.121
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] -0.375 0.517 -0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.633 r_dihedral_angle_4_deg 14.429 r_dihedral_angle_3_deg 12.151 r_dihedral_angle_1_deg 6.085 r_scangle_it 3.232 r_mcangle_it 2.907 r_scbond_it 2.466 r_mcbond_it 2.432 r_angle_refined_deg 1.488 r_angle_other_deg 1.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.633 r_dihedral_angle_4_deg 14.429 r_dihedral_angle_3_deg 12.151 r_dihedral_angle_1_deg 6.085 r_scangle_it 3.232 r_mcangle_it 2.907 r_scbond_it 2.466 r_mcbond_it 2.432 r_angle_refined_deg 1.488 r_angle_other_deg 1.139 r_mcbond_other 0.687 r_symmetry_vdw_other 0.269 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.21 r_nbd_other 0.194 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.108 r_symmetry_hbond_refined 0.106 r_nbtor_other 0.086 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2568 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 72
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ARP/wARP model building MolProbity model building