☰ Navigation Tabs
Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3 and lipid substrate GGPP
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 7.2 284 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 2.2 44.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.448 α = 90 b = 84.582 β = 90 c = 117.973 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 2008-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0000 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 2.35 30 99.4 0.063 17.5 4.9 28375 28201 5 42.4
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 2.35 2.45 99 0.377 7.1 5 3230
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DSS 2.35 30 26810 1403 99.5 0.19095 0.18761 0.25551 0.2617 RANDOM 37.329
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] -1.18 1.47 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.004 r_dihedral_angle_3_deg 19.375 r_dihedral_angle_4_deg 18.32 r_dihedral_angle_1_deg 7.416 r_scangle_it 5.164 r_angle_other_deg 4.262 r_mcbond_other 4.144 r_scbond_it 3.523 r_mcangle_it 2.638 r_angle_refined_deg 1.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.004 r_dihedral_angle_3_deg 19.375 r_dihedral_angle_4_deg 18.32 r_dihedral_angle_1_deg 7.416 r_scangle_it 5.164 r_angle_other_deg 4.262 r_mcbond_other 4.144 r_scbond_it 3.523 r_mcangle_it 2.638 r_angle_refined_deg 1.622 r_mcbond_it 1.567 r_symmetry_vdw_other 0.288 r_symmetry_hbond_refined 0.269 r_nbd_other 0.256 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.22 r_symmetry_vdw_refined 0.218 r_nbtor_refined 0.188 r_symmetry_metal_ion_refined 0.183 r_nbtor_other 0.114 r_chiral_restr 0.096 r_metal_ion_refined 0.047 r_bond_refined_d 0.018 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4920 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 69
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling