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Crystal Structure of mouse Rab27b bound to GDP in monoclinic space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IEZ PDB ENTRY 2IEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 289 MPD, Cacodylate, pH 5.5, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3 63.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.96 α = 90 b = 64.755 β = 90 c = 153.327 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 QUAMTUM 4r 2006-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0000 Photon Factory BL-6A
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 2.8 76.69 99.7 0.109 6.5 14358 1 1
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 2.8 2.9 97.4 97.4 0.418 5.2 1367
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2IEZ 2.8 40.1 13384 704 99.93 0.263 0.26163 0.25903 0.2565 0.31492 0.314 RANDOM 41.486
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] -1.34 4.24 -2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_4_deg 17.035 r_dihedral_angle_3_deg 16.671 r_dihedral_angle_1_deg 5.492 r_scangle_it 1.545 r_angle_refined_deg 1.067 r_scbond_it 0.897 r_mcangle_it 0.826 r_mcbond_it 0.469 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_4_deg 17.035 r_dihedral_angle_3_deg 16.671 r_dihedral_angle_1_deg 5.492 r_scangle_it 1.545 r_angle_refined_deg 1.067 r_scbond_it 0.897 r_mcangle_it 0.826 r_mcbond_it 0.469 r_nbtor_refined 0.305 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.153 r_symmetry_vdw_refined 0.128 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.07 r_metal_ion_refined 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2849 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 58
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction