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Crystal structure of a PROBABLE RIBOFLAVIN SYNTHASE, BETA CHAIN RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae
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 VAPOR DIFFUSION, SITTING DROP 8.5 290 MD Morpheus screen C12: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 30mM sodium-nitrate, 30mM di-sodium hydrogen phosphate, 30mM ammonium sulfate, 100mM Bicine/Trizma base pH 8.5; MyleA.00730.a.A1.PS00659 at 20mg/ml; direct cryo, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.71 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.95 α = 90 b = 109.95 β = 90 c = 288.33 γ = 120
Symmetry Space Group P 65 2 2
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 RIGAKU SATURN 944+ 2011-01-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.95 50 99.6 0.121 19.05 17.9 76305 75991 -3 27.672
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 1.95 2 96.4 0.523 4.16 8.15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1W19 1.95 45.25 76305 71727 3829 99.6 0.2101 0.2101 0.2081 0.2144 0.2461 0.2501 RANDOM 22.737
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] -0.05 -0.05 -0.05 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.971 r_dihedral_angle_4_deg 14.554 r_dihedral_angle_3_deg 13.141 r_dihedral_angle_1_deg 5.597 r_angle_refined_deg 1.521 r_mcangle_it 1.502 r_mcbond_it 0.939 r_mcbond_other 0.938 r_angle_other_deg 0.778 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.971 r_dihedral_angle_4_deg 14.554 r_dihedral_angle_3_deg 13.141 r_dihedral_angle_1_deg 5.597 r_angle_refined_deg 1.521 r_mcangle_it 1.502 r_mcbond_it 0.939 r_mcbond_other 0.938 r_angle_other_deg 0.778 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5354 Nucleic Acid Atoms Solvent Atoms 467 Heterogen Atoms 35
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction