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Engineered RabGGTase in complex with BMS analogue 13
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 2.33 47.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.625 α = 90 b = 90.741 β = 90 c = 115.539 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 MARMOSAIC 225 mm CCD 2009-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9879 SLS X10SA
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 1.95 19.99 98.7 0.062 16.9 4.9 51813 51134 32.1
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 1.95 2 98.4 0.361 5.2 4.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DSS 1.95 19.99 51813 48526 2565 98.73 0.17045 0.16835 0.21143 0.2258 RANDOM 27.672
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] 0.92 -0.64 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.14 r_dihedral_angle_4_deg 19.991 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_1_deg 5.341 r_angle_other_deg 4.188 r_scangle_it 3.581 r_scbond_it 2.291 r_mcbond_other 2.193 r_mcangle_it 1.791 r_angle_refined_deg 1.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.14 r_dihedral_angle_4_deg 19.991 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_1_deg 5.341 r_angle_other_deg 4.188 r_scangle_it 3.581 r_scbond_it 2.291 r_mcbond_other 2.193 r_mcangle_it 1.791 r_angle_refined_deg 1.121 r_mcbond_it 1.024 r_symmetry_vdw_other 0.27 r_nbd_other 0.233 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.212 r_xyhbond_nbd_other 0.202 r_symmetry_vdw_refined 0.2 r_symmetry_hbond_refined 0.186 r_nbtor_refined 0.177 r_nbtor_other 0.106 r_chiral_restr 0.072 r_metal_ion_refined 0.071 r_symmetry_metal_ion_refined 0.059 r_bond_refined_d 0.009 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_metal_ion_other r_symmetry_hbond_other 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 4986 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 48
Software Software Software Name Purpose MOSFLM data reduction PHASES phasing REFMAC refinement XDS data reduction XSCALE data scaling