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Engineered RabGGTase in complex with BMS analogue 16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 285 RabGGTase in 20mM Hepes pH7.2, 100mM NaCl and 2mM DTT was mixed with 15% PEG3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2. The obtained crystals was soaked with 20% PEG3350, 0.2M Ca Acetate, 5% Glycerol in the presence of 1mM inhibitor for 12 hour, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.636 α = 90 b = 91.366 β = 90 c = 114.093 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 IMAGE PLATE RIGAKU 2009-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.45 20 98.3 0.072 17.4 3.9 26269 25813 36.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.55 97.8 0.378 4.1 3.9
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 (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 3DSS 2.45 19.99 26269 24553 1259 98.51 0.18582 0.18264 0.1887 0.24771 0.2543 RANDOM 36.071
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] 0.39 -0.05 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.872 r_dihedral_angle_4_deg 18.024 r_dihedral_angle_3_deg 16.89 r_dihedral_angle_1_deg 6.05 r_angle_other_deg 4.214 r_scangle_it 3.933 r_scbond_it 2.778 r_mcangle_it 1.742 r_angle_refined_deg 1.544 r_mcbond_it 1.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.872 r_dihedral_angle_4_deg 18.024 r_dihedral_angle_3_deg 16.89 r_dihedral_angle_1_deg 6.05 r_angle_other_deg 4.214 r_scangle_it 3.933 r_scbond_it 2.778 r_mcangle_it 1.742 r_angle_refined_deg 1.544 r_mcbond_it 1.007 r_mcbond_other 0.423 r_symmetry_vdw_other 0.273 r_nbd_refined 0.246 r_nbd_other 0.239 r_xyhbond_nbd_refined 0.204 r_nbtor_refined 0.193 r_symmetry_vdw_refined 0.135 r_metal_ion_refined 0.134 r_nbtor_other 0.107 r_chiral_restr 0.089 r_symmetry_hbond_refined 0.068 r_bond_refined_d 0.015 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4994 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 46
Software Software Software Name Purpose MOSFLM data reduction PHASES phasing REFMAC refinement XDS data reduction XSCALE data scaling