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Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (TM1393) from Thermotoga maritima at 2.67 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VGZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 8 277 0.2M Ca(OAc)2, 10.0% PEG-8000, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.18 61.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.23 α = 90 b = 144.23 β = 90 c = 53.724 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 APS sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2004-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 2.67 49.35 98.28 0.109 11.46 4.51 18105 53.97
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) 1 2.67 2.77 98.23 0.523 1.97 3.66 1772
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 1vgz 2.67 49.35 16781 1313 98.26 0.20234 0.19879 0.2082 0.24783 0.2565 RANDOM 32.048
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] 1.9 0.95 1.9 -2.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.267 r_dihedral_angle_3_deg 16.021 r_dihedral_angle_4_deg 13.369 r_dihedral_angle_1_deg 6.071 r_scangle_it 1.617 r_angle_refined_deg 1.405 r_scbond_it 0.984 r_angle_other_deg 0.778 r_mcangle_it 0.672 r_mcbond_it 0.411
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.267 r_dihedral_angle_3_deg 16.021 r_dihedral_angle_4_deg 13.369 r_dihedral_angle_1_deg 6.071 r_scangle_it 1.617 r_angle_refined_deg 1.405 r_scbond_it 0.984 r_angle_other_deg 0.778 r_mcangle_it 0.672 r_mcbond_it 0.411 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.207 r_nbtor_refined 0.182 r_nbd_other 0.179 r_xyhbond_nbd_refined 0.173 r_symmetry_vdw_other 0.151 r_symmetry_hbond_refined 0.127 r_nbtor_other 0.085 r_mcbond_other 0.082 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3434 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 68
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement