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Crystal structure of Methylglyoxal synthase (TM1185) from Thermotoga maritima at 2.06 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B93
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 5.5 277 15.0% Ethanol, 0.2M Li2SO4, 0.1M Citrate pH 5.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.243 α = 90 b = 130.243 β = 90 c = 130.243 γ = 90
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 2004-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.05 91.89 98.4 0.111 9.2 5 22616 44.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 87.4 0.701 0.8 2 1449
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 1b93 2.06 91.89 21411 1163 98.03 0.16998 0.16732 0.1775 0.21884 0.2294 RANDOM 40.559
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.898 r_dihedral_angle_4_deg 16.375 r_dihedral_angle_3_deg 16.318 r_scangle_it 7.411 r_dihedral_angle_1_deg 6.145 r_scbond_it 5.323 r_mcangle_it 2.922 r_mcbond_it 2.293 r_angle_refined_deg 1.57 r_angle_other_deg 0.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.898 r_dihedral_angle_4_deg 16.375 r_dihedral_angle_3_deg 16.318 r_scangle_it 7.411 r_dihedral_angle_1_deg 6.145 r_scbond_it 5.323 r_mcangle_it 2.922 r_mcbond_it 2.293 r_angle_refined_deg 1.57 r_angle_other_deg 0.885 r_mcbond_other 0.673 r_symmetry_vdw_other 0.229 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.191 r_nbd_other 0.178 r_nbtor_refined 0.173 r_symmetry_hbond_refined 0.165 r_symmetry_vdw_refined 0.115 r_chiral_restr 0.096 r_nbtor_other 0.083 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2488 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 12
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling