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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 5.6 298 10% glycerol, magnesium sulphate, 20% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.676 α = 90 b = 54.833 β = 99.66 c = 88.506 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2003-03-11 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) 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 50 47.6 15989 2 2.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.57 91.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2.5 50 2.2 15989 15127 814 91.78 0.289 0.213 0.208 0.2107 0.291 0.2871 RANDOM 48.536
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] 7.45 -0.88 -3 -4.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.257 r_dihedral_angle_3_deg 18.536 r_dihedral_angle_4_deg 18.384 r_dihedral_angle_1_deg 5.776 r_scangle_it 2.182 r_angle_refined_deg 1.378 r_scbond_it 1.347 r_mcangle_it 1.086 r_mcbond_it 0.687 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.257 r_dihedral_angle_3_deg 18.536 r_dihedral_angle_4_deg 18.384 r_dihedral_angle_1_deg 5.776 r_scangle_it 2.182 r_angle_refined_deg 1.378 r_scbond_it 1.347 r_mcangle_it 1.086 r_mcbond_it 0.687 r_nbtor_refined 0.303 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.215 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.093 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3546 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 76
Software Software Software Name Purpose MOSFLM data reduction DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection