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The Crystal Structure of Methylglyoxal Synthase from Thermus sp. GH5 Bound to Phosphate Ion.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WO8 PDB ENTRY 1WO8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8 277 CRYSTALS WERE OBTAINED USING MICROBATCH METHOD AT 4C. CRYSTALLIZATION DROPS WERE MADE BY MIXING 2 MICROLITER OF A 7.8 MG/ML PROTEIN SOLUTION IN 50 MM TRIS-HCL, 300 MM NACL, 160 MM IMIDAZOLE AND 20% GLYCEROL WITH EQUAL AMOUNT OF CRYSTALLIZATION SOLUTION CONTAINING 0.1 M TRIS-HCL (PH 8.0), 29% W/V POLYETHYLENE GLYCOL (PEG) 4000.
Crystal Properties Matthews coefficient Solvent content 2.16 43.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.636 α = 90 b = 115.172 β = 90 c = 120.431 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC CCD MIRRORS 2009-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
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 1.08 42.2 96.6 0.05 12 3.6 156269
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 1.08 1.12 81.1 0.54 1.8 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FREE R-VALUE PDB ENTRY 1WO8 1.08 42.2 148053 7806 96.6 0.129 0.129 0.1362 0.161 0.1606 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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 58 2925.64 3293.85
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.109 s_non_zero_chiral_vol 0.093 s_zero_chiral_vol 0.092 s_anti_bump_dis_restr 0.083 s_similar_adp_cmpnt 0.051 s_angle_d 0.034 s_from_restr_planes 0.03 s_bond_d 0.015 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2903 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 15
Software Software Software Name Purpose SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing