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Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 284 14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties Matthews coefficient Solvent content 2.3 46.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.554 α = 90 b = 90.583 β = 90 c = 114.61 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 2008-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9764 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 1.95 30 99 0.048 19.7 4.1 51239 50703 5 31.8
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 1.95 2.05 98.6 0.331 5.5 4.2 6920
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DSS 1.95 29.4 48147 2542 98.97 0.18469 0.18227 0.23191 0.2388 RANDOM 29.089
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] -0.07 0.16 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.35 r_dihedral_angle_4_deg 16.112 r_dihedral_angle_3_deg 14.688 r_dihedral_angle_1_deg 5.474 r_angle_other_deg 4.158 r_scangle_it 3.455 r_mcbond_other 2.735 r_scbond_it 2.296 r_mcangle_it 1.811 r_angle_refined_deg 1.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.35 r_dihedral_angle_4_deg 16.112 r_dihedral_angle_3_deg 14.688 r_dihedral_angle_1_deg 5.474 r_angle_other_deg 4.158 r_scangle_it 3.455 r_mcbond_other 2.735 r_scbond_it 2.296 r_mcangle_it 1.811 r_angle_refined_deg 1.171 r_mcbond_it 1.063 r_symmetry_vdw_other 0.354 r_symmetry_vdw_refined 0.243 r_nbd_other 0.229 r_nbd_refined 0.214 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.163 r_metal_ion_refined 0.126 r_nbtor_other 0.106 r_chiral_restr 0.075 r_symmetry_metal_ion_refined 0.049 r_bond_refined_d 0.01 r_gen_planes_other 0.006 r_gen_planes_refined 0.004 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4991 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 56
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling