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Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with mono-prenylated peptide Ser-Cys(GG)-Ser-Cys derivated from Rab7
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) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties Matthews coefficient Solvent content 2.31 46.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.051 α = 90 b = 90.908 β = 90 c = 114.343 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 2007-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9825 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 2.15 29.4 99.1 0.072 15.2 4 38746 38414 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) 2.15 2.25 99.8 0.373 5.2 4.1 4857
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 2.15 29.21 36498 1916 99.2 0.17278 0.1698 0.179 0.23154 0.2408 RANDOM 36.193
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] 0.37 1.09 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.281 r_dihedral_angle_4_deg 19.081 r_dihedral_angle_3_deg 17.231 r_dihedral_angle_1_deg 11.459 r_scangle_it 4.269 r_angle_other_deg 3.733 r_mcbond_other 3.221 r_scbond_it 2.759 r_mcangle_it 2.44 r_angle_refined_deg 1.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.281 r_dihedral_angle_4_deg 19.081 r_dihedral_angle_3_deg 17.231 r_dihedral_angle_1_deg 11.459 r_scangle_it 4.269 r_angle_other_deg 3.733 r_mcbond_other 3.221 r_scbond_it 2.759 r_mcangle_it 2.44 r_angle_refined_deg 1.446 r_mcbond_it 1.391 r_symmetry_hbond_refined 0.416 r_nbd_other 0.23 r_nbd_refined 0.22 r_symmetry_vdw_other 0.214 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.179 r_metal_ion_refined 0.162 r_chiral_restr 0.136 r_symmetry_vdw_refined 0.126 r_nbtor_other 0.107 r_bond_refined_d 0.012 r_gen_planes_other 0.007 r_gen_planes_refined 0.005 r_bond_other_d 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 5095 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing