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Mycobacterium tuberculosis 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) in complex with CDPME
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PYD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1M Bis-Tris propane (pH 7.5), 1.5M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.29 62.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.762 α = 90 b = 73.693 β = 90 c = 106.229 γ = 90
Symmetry Space Group P 21 21 21
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 270 2009-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
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 60.52 99 28827 28610
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 3PYD 2 40 27107 1441 99.83 0.21819 0.21633 0.2112 0.25372 0.2434 RANDOM 30.297
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] 1.03 -0.22 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.058 r_dihedral_angle_3_deg 19.936 r_dihedral_angle_4_deg 18.759 r_dihedral_angle_1_deg 7.356 r_scangle_it 5.626 r_scbond_it 3.614 r_mcangle_it 2.313 r_angle_refined_deg 2.198 r_mcbond_it 1.306 r_chiral_restr 0.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.058 r_dihedral_angle_3_deg 19.936 r_dihedral_angle_4_deg 18.759 r_dihedral_angle_1_deg 7.356 r_scangle_it 5.626 r_scbond_it 3.614 r_mcangle_it 2.313 r_angle_refined_deg 2.198 r_mcbond_it 1.306 r_chiral_restr 0.234 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2166 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 33
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling