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Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with geranylgeranyl 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 2.32 46.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.264 α = 90 b = 90.618 β = 90 c = 114.478 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 2006-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0007 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 99.4 0.044 24.6 4.6 55872 55563 5 47
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 99.4 0.308 5.4 4.5 7804
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 29.21 52773 2790 99.48 0.18216 0.18024 0.2048 0.21953 0.2457 RANDOM 37.192
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 34.853 r_dihedral_angle_4_deg 19.517 r_dihedral_angle_3_deg 16.229 r_dihedral_angle_1_deg 10.728 r_scangle_it 2.999 r_scbond_it 2.064 r_mcangle_it 1.497 r_angle_refined_deg 1.375 r_mcbond_it 0.936 r_angle_other_deg 0.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.853 r_dihedral_angle_4_deg 19.517 r_dihedral_angle_3_deg 16.229 r_dihedral_angle_1_deg 10.728 r_scangle_it 2.999 r_scbond_it 2.064 r_mcangle_it 1.497 r_angle_refined_deg 1.375 r_mcbond_it 0.936 r_angle_other_deg 0.903 r_metal_ion_refined 0.506 r_mcbond_other 0.346 r_symmetry_hbond_refined 0.298 r_symmetry_vdw_other 0.217 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.199 r_nbd_other 0.187 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.095 r_nbtor_other 0.086 r_bond_refined_d 0.01 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 5055 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing