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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 2IEY PDB ENTRY 2IEY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 289 MPD, CaCl2, Hepes, pH 7.0, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.18 43.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.496 α = 90 b = 63.348 β = 98.45 c = 80.845 γ = 90
Symmetry Space Group C 1 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 CCD ADSC QUANTUM 315 2005-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.71 84.21 86.2 0.121 3 20069 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 2.7 2.8 76.4 0.484 2.2 1770
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 (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 2IEY 2.8 35.6 17648 952 87.36 0.26743 0.2623 0.2582 0.36315 0.3537 RANDOM 56.422
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] 3.19 -0.06 2.59 -5.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.34 r_dihedral_angle_3_deg 19.044 r_dihedral_angle_4_deg 15.57 r_dihedral_angle_1_deg 5.713 r_scangle_it 1.475 r_angle_refined_deg 1.189 r_scbond_it 0.884 r_mcangle_it 0.849 r_mcbond_it 0.478 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.34 r_dihedral_angle_3_deg 19.044 r_dihedral_angle_4_deg 15.57 r_dihedral_angle_1_deg 5.713 r_scangle_it 1.475 r_angle_refined_deg 1.189 r_scbond_it 0.884 r_mcangle_it 0.849 r_mcbond_it 0.478 r_nbtor_refined 0.306 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.075 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_refined 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 5600 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 116
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction CCP4 data scaling