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Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with farnesyl pyrophosphate
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 2.3 46.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.875 α = 90 b = 90.877 β = 90 c = 114.24 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 2007-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9998 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 1.9 29.4 98.2 0.046 22.5 5.7 55583 54566 5 34
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) 1.9 2 98.1 0.402 4.8 5.8 7660
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 1.9 29.19 51834 2731 98.21 0.16204 0.15927 0.1849 0.21548 0.2357 RANDOM 25.392
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 35.089 r_dihedral_angle_4_deg 17.573 r_dihedral_angle_3_deg 16.524 r_dihedral_angle_1_deg 10.116 r_scangle_it 3.58 r_scbond_it 2.336 r_mcangle_it 1.82 r_angle_refined_deg 1.409 r_mcbond_it 1.119 r_angle_other_deg 0.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.089 r_dihedral_angle_4_deg 17.573 r_dihedral_angle_3_deg 16.524 r_dihedral_angle_1_deg 10.116 r_scangle_it 3.58 r_scbond_it 2.336 r_mcangle_it 1.82 r_angle_refined_deg 1.409 r_mcbond_it 1.119 r_angle_other_deg 0.964 r_mcbond_other 0.525 r_xyhbond_nbd_other 0.25 r_symmetry_hbond_refined 0.249 r_nbd_refined 0.219 r_symmetry_vdw_other 0.205 r_nbd_other 0.19 r_nbtor_refined 0.181 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.127 r_symmetry_metal_ion_refined 0.124 r_nbtor_other 0.086 r_metal_ion_refined 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5023 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing