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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)butane 1-phosphate
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 = 131.37 α = 90 b = 80.758 β = 120.18 c = 85.965 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 2.3 25 98 0.1 8.4 2 33906 1
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 2.3 2.33 94.4 0.62 5.6 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.3 25.5 32208 1697 97.9 0.178 0.174 0.1836 0.268 0.2708 RANDOM 11.5
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] -1.5 -1.42 0.83 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.356 r_scangle_it 3.733 r_scbond_it 2.31 r_angle_refined_deg 1.901 r_mcangle_it 1.41 r_angle_other_deg 1.051 r_mcbond_it 0.778 r_symmetry_vdw_refined 0.359 r_symmetry_vdw_other 0.346 r_symmetry_hbond_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.356 r_scangle_it 3.733 r_scbond_it 2.31 r_angle_refined_deg 1.901 r_mcangle_it 1.41 r_angle_other_deg 1.051 r_mcbond_it 0.778 r_symmetry_vdw_refined 0.359 r_symmetry_vdw_other 0.346 r_symmetry_hbond_refined 0.309 r_nbd_refined 0.269 r_nbd_other 0.241 r_xyhbond_nbd_refined 0.231 r_chiral_restr 0.108 r_nbtor_other 0.092 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 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 5283 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms 187
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing