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structure of Rab8 in complex with MSS4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HXR PDB ENTRY 1hxr
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 20% PEG3350, 50mM TrisHCL pH 9.0, 0.2M magnesium acetate, 0.15% (w/v) 1,2,3-heptanetriole, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 48.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.92 α = 102.88 b = 49.85 β = 97.46 c = 83.48 γ = 90.12
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 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.934 ESRF ID14-2
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 2 19.17 94.5 40718 40718 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.05 74.6
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 1hxr 2 19.17 38678 38678 2036 0.19964 0.19964 0.1969 0.1975 0.25213 0.2502 RANDOM 44.426
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.436 r_dihedral_angle_4_deg 21.321 r_dihedral_angle_3_deg 16.551 r_dihedral_angle_1_deg 6.417 r_scangle_it 3.299 r_scbond_it 2.165 r_mcangle_it 1.824 r_angle_refined_deg 1.325 r_mcbond_it 1.123 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.436 r_dihedral_angle_4_deg 21.321 r_dihedral_angle_3_deg 16.551 r_dihedral_angle_1_deg 6.417 r_scangle_it 3.299 r_scbond_it 2.165 r_mcangle_it 1.824 r_angle_refined_deg 1.325 r_mcbond_it 1.123 r_nbtor_refined 0.303 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.194 r_symmetry_hbond_refined 0.179 r_symmetry_vdw_refined 0.159 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4162 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data scaling CNS phasing