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CRYSTAL STRUCTURE OF THE APO FORM OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I52 PDB ENTRY 1I52
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 279 PEG 8000, CALCIUM ACETATE, MAGNESIUM CHLORIDE, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.27 45.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.297 α = 90 b = 47.328 β = 94.18 c = 38.146 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 4 double crystal monochromator 2000-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.08 SSRL BL9-2
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 1.55 90 90.3 2.6 32.7 3.2 33935 30652 2 2 22.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 51.8 0.268 26.8 2.1 880
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1I52 1.55 33.93 1135780.99 32139 30590 1549 90.4 0.245 0.245 0.245 0.2456 0.265 0.2663 RANDOM 27.6
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] -4.74 0.61 4.72 0.01
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.8 c_scangle_it 3.37 c_mcangle_it 2.51 c_scbond_it 2.27 c_mcbond_it 1.64 c_angle_deg 1.2 c_improper_angle_d 0.82 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1624 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 1
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing