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Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase complexed with a CDP derived fluorescent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GX1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 290 0.1M ammonium sulfate, 10% PEG 200 MME, 0.1M sodium acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.68 53.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.033 α = 90 b = 115.269 β = 90.18 c = 87.609 γ = 90
Symmetry Space Group P 1 21 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 210 mirror 2004-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9756 ESRF ID29
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 2.3 29.5 99.4 0.097 10.1 3.5 47682 47420 3.9 29.85
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) 2.3 2.42 99.7 0.272 3.9 3.6 6904
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1GX1 2.3 29.5 47682 45024 2397 99.5 0.2582 0.24516 0.24327 0.2421 0.27952 0.2798 RANDOM 32.618
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] -3.19 0.24 6.86 -3.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.718 r_dihedral_angle_3_deg 14.84 r_dihedral_angle_4_deg 14.666 r_dihedral_angle_1_deg 4.979 r_angle_refined_deg 0.998 r_scangle_it 0.968 r_mcangle_it 0.594 r_scbond_it 0.518 r_mcbond_it 0.336 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.718 r_dihedral_angle_3_deg 14.84 r_dihedral_angle_4_deg 14.666 r_dihedral_angle_1_deg 4.979 r_angle_refined_deg 0.998 r_scangle_it 0.968 r_mcangle_it 0.594 r_scbond_it 0.518 r_mcbond_it 0.336 r_nbtor_refined 0.294 r_symmetry_vdw_refined 0.182 r_nbd_refined 0.173 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.06 r_metal_ion_refined 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6996 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 266
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing