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Structure of 4-diphosphocytidyl-2C-methyl-D-erythritol synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1INI PDB ENTRY 1INI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 0.2M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE, PH 5.6, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.23 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.604 α = 90 b = 73.604 β = 90 c = 175.562 γ = 90
Symmetry Space Group P 41 21 2
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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 20 99.5 0.03 37 4 19619 1.5
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) 1 2.4 2.46 98.6 0.27 3.1
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 PDB ENTRY 1INI 2.4 20 18554 1000 99.7 0.241 0.237 0.2306 0.333 0.3213 RANDOM 49.08
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] 1.21 1.21 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.195 r_scangle_it 3.784 r_scbond_it 2.35 r_mcangle_it 1.737 r_angle_refined_deg 1.668 r_mcbond_it 0.944 r_symmetry_vdw_refined 0.28 r_symmetry_hbond_refined 0.267 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.195 r_scangle_it 3.784 r_scbond_it 2.35 r_mcangle_it 1.737 r_angle_refined_deg 1.668 r_mcbond_it 0.944 r_symmetry_vdw_refined 0.28 r_symmetry_hbond_refined 0.267 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3307 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing