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Crystal structure of human RAB1A in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YZN pdb entries 1YZN, 1UKV experimental model PDB 1UKV pdb entries 1YZN, 1UKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 25% PEG3350, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.79 α = 90 b = 75.79 β = 90 c = 49.08 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 IV++ 2006-01-09 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 2.62 30 100 0.088 10.6 5102
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 2.62 2.71 100 0.826 10.5
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 pdb entries 1YZN, 1UKV 2.631 30 5048 233 99.98 0.201 0.199 0.2418 0.2523 0.23 36.747
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] -0.603 -0.302 -0.603 0.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.02 r_dihedral_angle_4_deg 24.925 r_dihedral_angle_3_deg 16.052 r_dihedral_angle_1_deg 4.754 r_scangle_it 1.662 r_angle_refined_deg 1.397 r_scbond_it 0.99 r_angle_other_deg 0.797 r_scangle_other 0.753 r_mcangle_it 0.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.02 r_dihedral_angle_4_deg 24.925 r_dihedral_angle_3_deg 16.052 r_dihedral_angle_1_deg 4.754 r_scangle_it 1.662 r_angle_refined_deg 1.397 r_scbond_it 0.99 r_angle_other_deg 0.797 r_scangle_other 0.753 r_mcangle_it 0.599 r_mcbond_it 0.459 r_scbond_other 0.287 r_symmetry_vdw_other 0.277 r_mcangle_other 0.268 r_symmetry_hbond_refined 0.227 r_nbd_refined 0.223 r_nbd_other 0.209 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.19 r_symmetry_vdw_refined 0.167 r_metal_ion_refined 0.137 r_nbtor_other 0.097 r_chiral_restr 0.075 r_mcbond_other 0.069 r_bond_refined_d 0.019 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 1240 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction