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Crystal structure of nucleotide-free Rab8:Rabin8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YZQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 293 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES. cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES), pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.58 65.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.645 α = 90 b = 165.301 β = 90 c = 166.404 γ = 90
Symmetry Space Group C 2 2 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 MARMOSAIC 225 mm CCD 2009-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.05 19.9 99.1 21895 21696 6.5 18.07
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 1YZQ 3.05 19.94 20544 1076 99.2 0.26537 0.26357 0.2586 0.29996 0.2926 RANDOM 94.485
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] 3.25 4.24 -7.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.719 r_dihedral_angle_3_deg 23.806 r_dihedral_angle_4_deg 19.38 r_dihedral_angle_1_deg 7.795 r_scangle_it 4.408 r_angle_other_deg 4.407 r_scbond_it 2.711 r_mcangle_it 2.666 r_mcbond_other 2.093 r_angle_refined_deg 1.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.719 r_dihedral_angle_3_deg 23.806 r_dihedral_angle_4_deg 19.38 r_dihedral_angle_1_deg 7.795 r_scangle_it 4.408 r_angle_other_deg 4.407 r_scbond_it 2.711 r_mcangle_it 2.666 r_mcbond_other 2.093 r_angle_refined_deg 1.688 r_mcbond_it 1.521 r_symmetry_hbond_refined 0.505 r_symmetry_vdw_other 0.318 r_symmetry_hbond_other 0.316 r_nbd_refined 0.271 r_nbd_other 0.238 r_symmetry_vdw_refined 0.21 r_nbtor_refined 0.205 r_xyhbond_nbd_refined 0.185 r_nbtor_other 0.115 r_chiral_restr 0.08 r_xyhbond_nbd_other 0.019 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d r_metal_ion_refined r_metal_ion_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4735 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 15
Software Software Software Name Purpose MOSFLM data reduction PHASES phasing REFMAC refinement XDS data reduction SCALEPACK data scaling