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Crystal Structure of Human RAB2B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OIV PDB ENTRY 1OIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 300 30% PEG5000, 02M Ammonium Sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.1 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.104 α = 90 b = 54.732 β = 90 c = 70.765 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 SBC-3 mirrors 2005-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.966 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 24.6 97.7 0.046 0.046 11.8 6.4 27473 27473 15.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.53 81 0.419 0.419 2.9 3.3 1127
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1OIV 1.501 24.6 26543 26543 878 97.66 0.19611 0.19611 0.19518 0.1913 0.22466 0.2231 RANDOM 17.043
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] -0.24 0.04 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.953 r_dihedral_angle_4_deg 17.448 r_dihedral_angle_3_deg 11.693 r_dihedral_angle_1_deg 5.464 r_scangle_it 3.133 r_scbond_it 2.004 r_mcangle_it 1.364 r_angle_refined_deg 1.285 r_mcbond_it 0.872 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.953 r_dihedral_angle_4_deg 17.448 r_dihedral_angle_3_deg 11.693 r_dihedral_angle_1_deg 5.464 r_scangle_it 3.133 r_scbond_it 2.004 r_mcangle_it 1.364 r_angle_refined_deg 1.285 r_mcbond_it 0.872 r_nbtor_refined 0.307 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.195 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 1415 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling MOLREP phasing