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Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 6)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DSS PDB entry 3DSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 284 14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties Matthews coefficient Solvent content 2.3 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.49 α = 90 b = 90.61 β = 90 c = 115.2 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 2006-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9816 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 2.25 30 97.6 0.052 18.03 4.9 33732 32922 4.9 43.7
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) 2.25 2.35 99.3 0.327 4.86 4.8 4004
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 3DSS 2.25 29.4 31280 1634 97.64 0.21016 0.20667 0.2141 0.27824 0.2855 RANDOM 46.788
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] 2.33 0.47 -2.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.915 r_dihedral_angle_4_deg 21.082 r_dihedral_angle_3_deg 18.577 r_dihedral_angle_1_deg 7.63 r_scangle_it 4.939 r_angle_other_deg 3.811 r_scbond_it 3.343 r_mcangle_it 2.979 r_mcbond_other 2.181 r_mcbond_it 1.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.915 r_dihedral_angle_4_deg 21.082 r_dihedral_angle_3_deg 18.577 r_dihedral_angle_1_deg 7.63 r_scangle_it 4.939 r_angle_other_deg 3.811 r_scbond_it 3.343 r_mcangle_it 2.979 r_mcbond_other 2.181 r_mcbond_it 1.779 r_angle_refined_deg 1.642 r_symmetry_vdw_other 0.282 r_symmetry_hbond_refined 0.235 r_nbd_other 0.231 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.205 r_xyhbond_nbd_refined 0.201 r_nbtor_refined 0.186 r_nbtor_other 0.111 r_chiral_restr 0.104 r_xyhbond_nbd_other 0.022 r_bond_refined_d 0.017 r_gen_planes_other 0.009 r_gen_planes_refined 0.006 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4918 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 47
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling