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30mer structure of Lumazine synthase from Salmonella typhimurium LT2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.75 293 1.6M Ammonium Sulfate, 100mM Tris buffer, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.9 57.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.43 α = 90 b = 157.49 β = 91.58 c = 202.788 γ = 90
Symmetry Space Group I 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 MAR scanner 345 mm plate Osmic VariMax 2009-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.542
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 3.5 134.03 66.5 0.258 3.2 2.2 45638 45638 72.4
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 3.5 3.69 70.2 0.392 2.2 2 7001
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3MK3 3.5 78.745 1.35 45631 1139 66.02 0.2562 0.2551 0.2664 0.2994 0.307 Random
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] -15.0135 -5.2719 -27.6241 -22.4199
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.503 f_angle_d 0.946 f_chiral_restr 0.058 f_bond_d 0.008 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33062 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 200
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing CCP4 model building PHENIX refinement MOSFLM data reduction SCALA data scaling CCP4 phasing