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The Crystal Structure of Methylglyoxal Synthase from Thermus sp. GH5 Bound to Malonate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X8V PDB ENTRY 2X8V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 CRYSTALS WERE OBTAINED USING THE HANGING-DROP VAPOR DIFFUSION TECHNIQUE AT 21C; DROPLETS CONTAINING 8 MG/ML PROTEIN IN 0.05 M TRIS-HCL, 0.3 M NACL, 0.097 M IMIDAZOLE AND 20% OF GLYCEROL WERE EQUILIBRATED OVER WELLS CONTAINING 1 M NA MALONATE (PH 6.0).
Crystal Properties Matthews coefficient Solvent content 4.69 73.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.83 α = 90 b = 109.83 β = 90 c = 75.74 γ = 120
Symmetry Space Group P 63 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 ADSC CCD MIRRORS 2009-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 47.56 99.9 0.01 16.3 10.4 20151 27.8
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 1.95 2.06 99.9 0.79 3.2 10.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2X8V 1.95 47.56 19116 1025 99.7 0.19369 0.19216 0.1943 0.22264 0.2217 RANDOM 31.116
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] 0.06 0.03 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.786 r_dihedral_angle_4_deg 15.986 r_dihedral_angle_3_deg 14.514 r_dihedral_angle_1_deg 5.582 r_scangle_it 3.679 r_scbond_it 2.501 r_mcangle_it 1.748 r_angle_refined_deg 1.706 r_mcbond_it 1.008 r_chiral_restr 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.786 r_dihedral_angle_4_deg 15.986 r_dihedral_angle_3_deg 14.514 r_dihedral_angle_1_deg 5.582 r_scangle_it 3.679 r_scbond_it 2.501 r_mcangle_it 1.748 r_angle_refined_deg 1.706 r_mcbond_it 1.008 r_chiral_restr 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 949 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing