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Crystal structure of 2,5-diketo-D-gluconic acid reductase (TM1009) from Thermotoga maritima at 2.40 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 5.6 277 5.0% Glycerol, 19.0% iso-Propanol, 19.0% PEG-4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.73 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.314 α = 90 b = 94.314 β = 90 c = 146.855 γ = 120
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 2004-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 2.4 24.93 99.9 0.123 15.6 7.4 28944 49.56
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 2.4 2.46 100 0.83 2.4 7.4 2124
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 REFINEMENT STARTING MODEL 2.4 24.93 27471 1471 99.89 0.15363 0.15113 0.1642 0.20258 0.2148 RANDOM 39.279
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] 0.93 0.46 0.93 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.999 r_dihedral_angle_4_deg 19.905 r_dihedral_angle_3_deg 15.738 r_dihedral_angle_1_deg 9.909 r_scangle_it 6.228 r_scbond_it 4.762 r_mcangle_it 2.406 r_angle_refined_deg 1.672 r_mcbond_it 1.616 r_angle_other_deg 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.999 r_dihedral_angle_4_deg 19.905 r_dihedral_angle_3_deg 15.738 r_dihedral_angle_1_deg 9.909 r_scangle_it 6.228 r_scbond_it 4.762 r_mcangle_it 2.406 r_angle_refined_deg 1.672 r_mcbond_it 1.616 r_angle_other_deg 0.94 r_mcbond_other 0.486 r_symmetry_vdw_other 0.35 r_symmetry_vdw_refined 0.251 r_nbd_refined 0.2 r_nbd_other 0.192 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.089 r_nbtor_other 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4560 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 96
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling