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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, 8% PEG 200 MME, 0.1M SODIUM ACETATE, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 6.7 81.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.098 α = 90 b = 145.098 β = 90 c = 145.098 γ = 90
Symmetry Space Group I 21 3
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 0.9330 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 28.5 99.8 17715 3
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 2.5 2.64 100 0.685 0.685 2.9 8.6
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 1GX1 2.5 30 16813 902 99.99 0.20855 0.20714 0.2218 0.2352 0.2298 RANDOM 51.34
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.065 r_dihedral_angle_3_deg 16.557 r_dihedral_angle_4_deg 14.748 r_dihedral_angle_1_deg 8.683 r_scangle_it 2.984 r_scbond_it 1.614 r_mcangle_it 1.482 r_angle_refined_deg 1.256 r_mcbond_it 0.923 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.065 r_dihedral_angle_3_deg 16.557 r_dihedral_angle_4_deg 14.748 r_dihedral_angle_1_deg 8.683 r_scangle_it 2.984 r_scbond_it 1.614 r_mcangle_it 1.482 r_angle_refined_deg 1.256 r_mcbond_it 0.923 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.216 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.093 r_metal_ion_refined 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1188 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 64
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling