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Crystal structure of RabGGTase(DELTA LRR; DELTA IG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LTX PDB ENTRY 1LTX
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 2.29 46.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.748 α = 90 b = 90.628 β = 90 c = 114.068 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 2006-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.98 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 1.8 30 99.3 0.063 16.4 4.6 64818 64333 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) 1.8 1.9 99.7 0.275 4.7 3.4 9571
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 1LTX 1.8 29.13 61099 3214 99.26 0.15108 0.14888 0.1611 0.19383 0.2024 RANDOM 17.742
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 37.169 r_dihedral_angle_4_deg 19.436 r_dihedral_angle_3_deg 15.566 r_dihedral_angle_1_deg 5.19 r_scangle_it 3.825 r_scbond_it 2.411 r_mcangle_it 1.86 r_angle_refined_deg 1.25 r_mcbond_it 1.157 r_mcbond_other 0.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.169 r_dihedral_angle_4_deg 19.436 r_dihedral_angle_3_deg 15.566 r_dihedral_angle_1_deg 5.19 r_scangle_it 3.825 r_scbond_it 2.411 r_mcangle_it 1.86 r_angle_refined_deg 1.25 r_mcbond_it 1.157 r_mcbond_other 0.956 r_angle_other_deg 0.863 r_nbd_refined 0.215 r_symmetry_vdw_other 0.202 r_nbd_other 0.187 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.159 r_symmetry_vdw_refined 0.134 r_symmetry_metal_ion_refined 0.116 r_symmetry_hbond_refined 0.114 r_metal_ion_refined 0.104 r_nbtor_other 0.086 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5125 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing