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Structure analysis of Geranyl diphosphate methyltransferase in complex with SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BUS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.75 293 1M ammonium suflate, 8% glycerol, 0.1M Tris-HCl, 10mM SAM, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.99 58.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.942 α = 90 b = 147.942 β = 90 c = 66.467 γ = 120
Symmetry Space Group P 63 2 2
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 315r mirrors 2008-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 50 98.8 0.06 28.8 7.4 22017 37.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 99.6 0.424 2.7 7.3 2174
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 3bus 2.2 33.23 21970 1146 98.6 0.261 0.261 0.2628 0.299 0.2742 RANDOM 64.8819
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] 15.41 15.41 -30.83
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_angle_deg 1.3 c_improper_angle_d 1.03 c_bond_d 0.008 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1937 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 20
Software Software Software Name Purpose ADSC data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling