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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) 1,1 difluoropentane-1- 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 = 131.384 α = 90 b = 81.251 β = 120.25 c = 85.883 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 1.9 20 95.9 0.05 13.5 2 58728 1 25.1
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 1.9 1.94 80.3 0.36 1.37 2.7
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 1.9 15 55681 2972 95.5 0.178 0.175 0.219 RANDOM 30.6
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] -1.75 -1.77 0.82 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.66 r_dihedral_angle_4_deg 16.943 r_dihedral_angle_3_deg 12.824 r_dihedral_angle_1_deg 4.742 r_scangle_it 2.678 r_scbond_it 1.583 r_angle_refined_deg 1.415 r_mcangle_it 0.919 r_mcbond_it 0.468 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.66 r_dihedral_angle_4_deg 16.943 r_dihedral_angle_3_deg 12.824 r_dihedral_angle_1_deg 4.742 r_scangle_it 2.678 r_scbond_it 1.583 r_angle_refined_deg 1.415 r_mcangle_it 0.919 r_mcbond_it 0.468 r_nbtor_refined 0.294 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.23 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 5269 Nucleic Acid Atoms Solvent Atoms 549 Heterogen Atoms 177
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing