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Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with di-prenylated peptide Ser-Cys(GG)-Ser-Cys(GG) derivated from Rab7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DSS DB ENTRY 3DSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 284 14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 2.5% (v/v)DMSO, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties Matthews coefficient Solvent content 2.33 47.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.354 α = 90 b = 91.153 β = 90 c = 114.591 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 2007-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9841 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 2.1 30 99.8 0.057 23.4 7.2 41909 41826 5 39
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) 2.1 2.2 100 0.391 6.9 7.4 5348
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 DB ENTRY 3DSS 2.1 29.37 39725 2101 99.85 0.17056 0.16753 0.1813 0.22942 0.24 RANDOM 30.065
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 33.612 r_dihedral_angle_4_deg 18.592 r_dihedral_angle_3_deg 16.294 r_dihedral_angle_1_deg 5.676 r_scangle_it 3.576 r_scbond_it 2.397 r_mcangle_it 1.867 r_angle_refined_deg 1.285 r_mcbond_it 1.166 r_angle_other_deg 0.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.612 r_dihedral_angle_4_deg 18.592 r_dihedral_angle_3_deg 16.294 r_dihedral_angle_1_deg 5.676 r_scangle_it 3.576 r_scbond_it 2.397 r_mcangle_it 1.867 r_angle_refined_deg 1.285 r_mcbond_it 1.166 r_angle_other_deg 0.846 r_mcbond_other 0.699 r_symmetry_hbond_refined 0.263 r_symmetry_vdw_other 0.262 r_nbd_refined 0.215 r_nbtor_refined 0.182 r_nbd_other 0.18 r_xyhbond_nbd_refined 0.175 r_symmetry_vdw_refined 0.156 r_metal_ion_refined 0.099 r_nbtor_other 0.087 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5089 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing