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Rat Protein Geranylgeranyltransferase Type-I Complexed with a GGPP analog and a KKKSKTKCVIM Peptide Derived from K-Ras4B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N4Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 291 1.3 M ammonium sulfate, 175 mM NaCitrate pH 6.5, 100 mM MES pH 6.3, 20 mM DTT, 1uM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 5.6 77.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 272.531 α = 90 b = 268.484 β = 131.48 c = 185.94 γ = 90
Symmetry Space Group C 1 2 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 MAR CCD 165 mm Elliptically bent mirror/sagittal focusing second monochromator crystal 2002-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.07172 APS 22-ID
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 30 92.2 0.065 12.3 2.5 272486 251777 -0.5 -0.5 60.7
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 79.2 0.193 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1N4Q 2.7 29.98 -0.5 272961 251777 12637 92.2 0.194 0.194 0.194 0.1933 0.211 0.2105 RANDOM 64.9
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] -8.55 -6.22 13.95 -5.4
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.2 c_scangle_it 3.33 c_mcangle_it 2.29 c_scbond_it 2.13 c_mcbond_it 1.34 c_angle_deg 1.2 c_improper_angle_d 0.8 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.2 c_scangle_it 3.33 c_mcangle_it 2.29 c_scbond_it 2.13 c_mcbond_it 1.34 c_angle_deg 1.2 c_improper_angle_d 0.8 c_bond_d 0.007 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 32406 Nucleic Acid Atoms Solvent Atoms 678 Heterogen Atoms 208
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing