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Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand
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 7.5 298 2M ammonium formate, HEPES, 5% butanediol, pH 7.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 7.152275 82.802673
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.498 α = 90 b = 144.498 β = 90 c = 144.498 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 mirrors 2003-02-01 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 Merge I (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 2.7 29.495 99.9 0.099 0.099 5.995 14.5 13946 8.9
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) 2.7 2.85 100 0.274 0.274 2.7 14.7 2025
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1GX1 2.7 24.69 13795 13786 690 99.93 0.186 0.184 0.218 0.2185 RANDOM 40.065
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 35.792 r_dihedral_angle_3_deg 19.381 r_dihedral_angle_4_deg 16.282 r_dihedral_angle_1_deg 6.139 r_scangle_it 2.979 r_scbond_it 1.764 r_mcangle_it 1.631 r_angle_refined_deg 1.551 r_mcbond_it 0.999 r_symmetry_vdw_refined 0.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.792 r_dihedral_angle_3_deg 19.381 r_dihedral_angle_4_deg 16.282 r_dihedral_angle_1_deg 6.139 r_scangle_it 2.979 r_scbond_it 1.764 r_mcangle_it 1.631 r_angle_refined_deg 1.551 r_mcbond_it 0.999 r_symmetry_vdw_refined 0.341 r_nbtor_refined 0.319 r_nbd_refined 0.237 r_symmetry_hbond_refined 0.183 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.091 r_metal_ion_refined 0.058 r_symmetry_metal_ion_refined 0.015 r_bond_refined_d 0.013 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1215 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 41
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction