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Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 0.5M ammonium sulphate, tri-sodium citrate, lithium sulphate monohydrate, pH 5.6, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 7.329383 83.218231
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.681 α = 90 b = 145.681 β = 90 c = 145.681 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 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2003-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.801 29.737 99.9 0.087 0.087 6.561 14.5 12830 12818 5
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) 2.8 2.95 100 0.476 0.476 1.6 14.8 1843
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 2.9 24.98 5 12818 11538 557 99.93 0.189 0.188 0.1928 0.209 0.2164 RANDOM 57.048
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.754 r_dihedral_angle_4_deg 21.8 r_dihedral_angle_3_deg 16.655 r_dihedral_angle_1_deg 9.234 r_scangle_it 8.508 r_scbond_it 5.158 r_mcangle_it 3.283 r_angle_refined_deg 2.329 r_mcbond_it 1.918 r_symmetry_hbond_refined 0.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.754 r_dihedral_angle_4_deg 21.8 r_dihedral_angle_3_deg 16.655 r_dihedral_angle_1_deg 9.234 r_scangle_it 8.508 r_scbond_it 5.158 r_mcangle_it 3.283 r_angle_refined_deg 2.329 r_mcbond_it 1.918 r_symmetry_hbond_refined 0.538 r_nbtor_refined 0.345 r_nbd_refined 0.285 r_symmetry_vdw_refined 0.284 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.169 r_bond_refined_d 0.029 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1175 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 40
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection