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Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R2Q pdb entry codes 1r2q 2qv2 experimental model PDB 2QV2 pdb entry codes 1r2q 2qv2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.147 α = 90 b = 55.34 β = 91.93 c = 173.836 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 MARMOSAIC 225 mm CCD 2009-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 47.378 98.3 0.055 99857
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 2.1 97 0.334 4.2
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 codes 1r2q 2qv2 2 47.378 99857 4996 98.27 0.2096 0.2079 0.2089 0.2411 0.241 RANDOM 39.609
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] -2.25 0.78 0.85 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.088 r_dihedral_angle_4_deg 20.549 r_dihedral_angle_3_deg 14.499 r_dihedral_angle_1_deg 4.919 r_scangle_it 4.164 r_scbond_it 2.706 r_mcangle_it 1.675 r_angle_refined_deg 1.412 r_mcbond_it 1.147 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.088 r_dihedral_angle_4_deg 20.549 r_dihedral_angle_3_deg 14.499 r_dihedral_angle_1_deg 4.919 r_scangle_it 4.164 r_scbond_it 2.706 r_mcangle_it 1.675 r_angle_refined_deg 1.412 r_mcbond_it 1.147 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.246 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.12 r_chiral_restr 0.099 r_metal_ion_refined 0.018 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9950 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling