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Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DCE PDB ENTRY 1DCE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 298 20% PEG 3350, 100mM KSCN, 100mM Namalonate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.05 59.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.7 α = 90 b = 197.3 β = 112.8 c = 85.3 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9393 ESRF ID14-1
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 2.7 19.7 94.5 0.094 9.5 3.6 54362 54362 53.8
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) 2.7 2.8 62.5 0.364 3.25 2.7 3716
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1DCE 2.7 19.74 54362 54362 2714 94.9 0.224 0.224 0.224 0.2241 0.272 0.225 RANDOM 52.4
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 c_dihedral_angle_d 22.8 c_scangle_it 2.82 c_improper_angle_d 2.37 c_mcangle_it 2.1 c_scbond_it 1.88 c_angle_deg 1.5 c_mcbond_it 1.25 c_bond_d 0.016 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_scangle_it 2.82 c_improper_angle_d 2.37 c_mcangle_it 2.1 c_scbond_it 1.88 c_angle_deg 1.5 c_mcbond_it 1.25 c_bond_d 0.016 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10754 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 17
Software Software Software Name Purpose ProDC data collection XDS data reduction CNS refinement XDS data scaling CNS phasing