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LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 4-(6- chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)butyl phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W19 PDB ENTRY 1W19
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.4 pH 6.40
Crystal Properties Matthews coefficient Solvent content 2.5 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.64 α = 90 b = 82.244 β = 120.53 c = 86.346 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 MARRESEACH MIRRORS 2005-07-16 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 96.5 0.11 8.2 3.4 51716 1 31.8
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 71.7 0.52 1.62 2.2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1W19 2 15 26051 1383 96.5 0.15 0.146 0.215 RANDOM 27.41
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] -2.02 -2.02 0.92 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.999 r_dihedral_angle_4_deg 17.051 r_dihedral_angle_3_deg 14.386 r_dihedral_angle_1_deg 5.171 r_scangle_it 3.113 r_scbond_it 1.789 r_angle_refined_deg 1.409 r_mcangle_it 1.007 r_mcbond_it 0.509 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.999 r_dihedral_angle_4_deg 17.051 r_dihedral_angle_3_deg 14.386 r_dihedral_angle_1_deg 5.171 r_scangle_it 3.113 r_scbond_it 1.789 r_angle_refined_deg 1.409 r_mcangle_it 1.007 r_mcbond_it 0.509 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.234 r_symmetry_hbond_refined 0.201 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 5294 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 182
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing