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Rat Protein Geranylgeranyltransferase Type-I Complexed with a GGPP analog and a RRCVLL Peptide Derived from Cdc42 splice isoform-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N4Q pdn entry 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 5.5 77.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 271.262 α = 90 b = 266.922 β = 131.91 c = 185.75 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 ADSC QUANTUM 315 Pt-coated toroidal Si mirror 2003-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1000 NSLS X25
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 2.9 30 91.4 0.067 11.9 2.5 212963 197897 -0.5 -0.5 41.3
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) 2.9 3 81 0.295 2.1
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 pdn entry 1N4Q 2.9 29.96 -0.5 216465 197897 9984 91.4 0.199 0.199 0.199 0.1958 0.218 0.2139 RANDOM 78.4
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] -12.34 -8.41 18.59 -6.24
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20 c_scangle_it 3.17 c_mcangle_it 2.13 c_scbond_it 2.02 c_mcbond_it 1.24 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 c_scangle_it 3.17 c_mcangle_it 2.13 c_scbond_it 2.02 c_mcbond_it 1.24 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 32422 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 195
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing