☰ Navigation Tabs
Crystal structure of human RAB3D in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RAB pdb entry 3RAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 20% PEG8000, 0.2M magnesium acetate, 0.1M sodium cacodylate, pH 6.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.9 30.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.7 α = 90 b = 63.222 β = 90 c = 67.695 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 IMAGE PLATE RIGAKU RAXIS 2006-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 1.53 28.25 88.3 0.035 32.8 7.4 21079
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) 1.53 1.58 28 0.056 1.8
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 3RAB 1.53 28.25 21035 1069 88.349 0.155 0.1533 0.1645 0.1854 0.1949 random 8.16
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] -0.293 0.166 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.992 r_dihedral_angle_4_deg 11.515 r_dihedral_angle_3_deg 11.213 r_dihedral_angle_1_deg 5.382 r_scangle_it 3.251 r_mcangle_it 2.418 r_scbond_it 2.183 r_mcbond_it 1.756 r_angle_refined_deg 1.344 r_angle_other_deg 0.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.992 r_dihedral_angle_4_deg 11.515 r_dihedral_angle_3_deg 11.213 r_dihedral_angle_1_deg 5.382 r_scangle_it 3.251 r_mcangle_it 2.418 r_scbond_it 2.183 r_mcbond_it 1.756 r_angle_refined_deg 1.344 r_angle_other_deg 0.874 r_mcbond_other 0.454 r_symmetry_vdw_other 0.333 r_nbd_refined 0.213 r_nbd_other 0.193 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.127 r_symmetry_vdw_refined 0.12 r_xyhbond_nbd_refined 0.116 r_nbtor_other 0.085 r_chiral_restr 0.078 r_bond_refined_d 0.015 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1438 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction