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Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YE7 PDB entry 1YE7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (6.36 mg/ml) AND RESERVOIR SOLUTION CONTAINING 0.9M Li Sulfate, 0.09M HEPES pH 8.0, 0.01M Betaine, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.34 63.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.084 α = 90 b = 104.084 β = 90 c = 107.76 γ = 120
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 RIGAKU JUPITER 210 2007-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.00000 SPring-8 BL26B2
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 2.2 50 100 0.043 25.6 11 33616
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) 2.2 2.28 100 0.286 11 3339
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 PDB entry 1YE7 2.2 50 33570 1699 99.94 0.228 0.227 0.2191 0.248 0.2399 RANDOM 37.878
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] 1.05 0.53 1.05 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.015 r_dihedral_angle_4_deg 20.604 r_dihedral_angle_3_deg 15.689 r_dihedral_angle_1_deg 8.895 r_scangle_it 3.451 r_scbond_it 2.048 r_angle_refined_deg 1.467 r_mcangle_it 1.426 r_mcbond_it 0.775 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.015 r_dihedral_angle_4_deg 20.604 r_dihedral_angle_3_deg 15.689 r_dihedral_angle_1_deg 8.895 r_scangle_it 3.451 r_scbond_it 2.048 r_angle_refined_deg 1.467 r_mcangle_it 1.426 r_mcbond_it 0.775 r_nbtor_refined 0.302 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.215 r_xyhbond_nbd_refined 0.168 r_symmetry_vdw_refined 0.167 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3006 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling EPMR phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction