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Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with mono-prenylated peptide Ser-Cys-Ser-Cys(GG) 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 46.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.035 α = 90 b = 90.613 β = 90 c = 114.376 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 0.9999 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 99.9 0.085 31 18.5 41395 41339 5 30
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 99.7 0.379 11.1 16.5 5293
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 2.1 29.2 39268 2071 99.92 0.15231 0.14927 0.1624 0.21114 0.2179 RANDOM 25.886
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] 1.73 -0.44 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.766 r_dihedral_angle_4_deg 19.937 r_dihedral_angle_3_deg 16.373 r_dihedral_angle_1_deg 12.981 r_angle_other_deg 3.745 r_scangle_it 3.701 r_scbond_it 2.394 r_mcangle_it 1.968 r_angle_refined_deg 1.456 r_mcbond_it 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.766 r_dihedral_angle_4_deg 19.937 r_dihedral_angle_3_deg 16.373 r_dihedral_angle_1_deg 12.981 r_angle_other_deg 3.745 r_scangle_it 3.701 r_scbond_it 2.394 r_mcangle_it 1.968 r_angle_refined_deg 1.456 r_mcbond_it 1.1 r_mcbond_other 1.034 r_symmetry_hbond_refined 0.443 r_nbd_other 0.234 r_symmetry_vdw_other 0.228 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.182 r_nbtor_other 0.107 r_chiral_restr 0.104 r_xyhbond_nbd_other 0.074 r_metal_ion_refined 0.059 r_symmetry_metal_ion_refined 0.017 r_bond_refined_d 0.011 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d r_metal_ion_other r_symmetry_hbond_other 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 5093 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing