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Crystal structure of human RAB25 in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OIX pdb entry 1OIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% peg-3350, 0.2M ammonium chloride, vapor diffusion, sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.15 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.25 α = 90 b = 90.25 β = 90 c = 45.598 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 2006-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 2.3 30 100 0.146 6.9 12.8 8824
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) 2.3 2.38 100 0.754 13
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 entry 1OIX 2.3 28.537 8778 418 99.943 0.21 0.2082 0.2061 0.2575 0.2483 36.904
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] -0.426 -0.426 0.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.243 r_dihedral_angle_4_deg 18.108 r_dihedral_angle_3_deg 13.333 r_dihedral_angle_1_deg 6.504 r_mcangle_it 4.087 r_scangle_it 3.971 r_scbond_it 2.877 r_mcbond_it 2.756 r_angle_refined_deg 1.474 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.243 r_dihedral_angle_4_deg 18.108 r_dihedral_angle_3_deg 13.333 r_dihedral_angle_1_deg 6.504 r_mcangle_it 4.087 r_scangle_it 3.971 r_scbond_it 2.877 r_mcbond_it 2.756 r_angle_refined_deg 1.474 r_nbtor_refined 0.298 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.176 r_symmetry_hbond_refined 0.144 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.094 r_metal_ion_refined 0.038 r_bond_refined_d 0.017 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1336 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 30
Software Software Software Name Purpose PHASER phasing DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction