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Engineered RabGGTase in complex with a peptidomimetic inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LTX PDB ENTRY 1LTX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 284 14% (w/v) PEG 3350, 0.2 M Ca-Acetate, 0.1 M HEPES, cocrystallization with 5 mM inhibitor, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties Matthews coefficient Solvent content 2.32 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.192 α = 90 b = 91.671 β = 90 c = 115.439 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 Si(111) monochromator 2006-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9797 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 2.3 20 99.7 5.2 20 5.7 31830 4.7 50
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 2.3 2.4 100 40.7 4.7 5.8 3742
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 1LTX 2.3 19.88 30241 1587 99.95 0.19242 0.18908 0.1938 0.25617 0.2629 RANDOM 31.217
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 37.575 r_dihedral_angle_4_deg 19.655 r_dihedral_angle_3_deg 18.289 r_dihedral_angle_1_deg 6.726 r_scangle_it 2.958 r_scbond_it 2.1 r_angle_refined_deg 1.622 r_mcangle_it 1.451 r_angle_other_deg 1.061 r_mcbond_it 0.878
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.575 r_dihedral_angle_4_deg 19.655 r_dihedral_angle_3_deg 18.289 r_dihedral_angle_1_deg 6.726 r_scangle_it 2.958 r_scbond_it 2.1 r_angle_refined_deg 1.622 r_mcangle_it 1.451 r_angle_other_deg 1.061 r_mcbond_it 0.878 r_symmetry_vdw_other 0.224 r_nbd_refined 0.217 r_nbd_other 0.195 r_mcbond_other 0.195 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.185 r_metal_ion_refined 0.158 r_symmetry_hbond_refined 0.103 r_nbtor_other 0.095 r_chiral_restr 0.093 r_symmetry_vdw_refined 0.084 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4988 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing