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Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)propane 1-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EJB PDB ENTRY 1EJB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 ADA BUFFER PH 6.4, 3.5M POTASSIUM ACETATE,0.5 M DTT,10%MPD
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.267 α = 90 b = 80.688 β = 120.29 c = 86.188 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 MARRESEARCH MIRRORS 2003-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 20 99.4 0.09 10.26 2.08 52169 1 20.8
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 2.02 99 0.51 3.38 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 1EJB 2 19.54 49503 2661 99.4 0.151 0.149 0.1773 0.194 0.2172 RANDOM 13.25
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] -1.74 -1.7 0.33 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.323 r_scangle_it 3.176 r_scbond_it 1.896 r_angle_refined_deg 1.81 r_mcangle_it 1.104 r_angle_other_deg 0.895 r_mcbond_it 0.597 r_symmetry_vdw_refined 0.454 r_symmetry_vdw_other 0.315 r_nbd_refined 0.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.323 r_scangle_it 3.176 r_scbond_it 1.896 r_angle_refined_deg 1.81 r_mcangle_it 1.104 r_angle_other_deg 0.895 r_mcbond_it 0.597 r_symmetry_vdw_refined 0.454 r_symmetry_vdw_other 0.315 r_nbd_refined 0.266 r_symmetry_hbond_refined 0.246 r_nbd_other 0.245 r_xyhbond_nbd_refined 0.212 r_chiral_restr 0.095 r_nbtor_other 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 5294 Nucleic Acid Atoms Solvent Atoms 631 Heterogen Atoms 226
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing