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Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-xylulose 5-phosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 298 16% MePEG 2000, 50 mM BTP pH 7.0, 5 mM MgCl2, microbatch, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.13 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.912 α = 90 b = 41.58 β = 96.41 c = 91.627 γ = 90
Symmetry Space Group C 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 CCD CUSTOM-MADE 2002-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9870 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.76 100 98.2 18.1 45531 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.76 1.82 98.1 2.62
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.76 91.29 45531 43255 2276 97.97 0.1915 0.18954 0.1981 0.22875 0.2352 RANDOM 26.359
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] -0.63 0.53 1.51 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.203 r_scangle_it 4.95 r_scbond_it 3.059 r_mcangle_it 1.973 r_angle_refined_deg 1.724 r_angle_other_deg 1.685 r_mcbond_it 1.086 r_symmetry_vdw_other 0.272 r_nbd_other 0.248 r_nbd_refined 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.203 r_scangle_it 4.95 r_scbond_it 3.059 r_mcangle_it 1.973 r_angle_refined_deg 1.724 r_angle_other_deg 1.685 r_mcbond_it 1.086 r_symmetry_vdw_other 0.272 r_nbd_other 0.248 r_nbd_refined 0.233 r_symmetry_hbond_refined 0.218 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.101 r_nbtor_other 0.083 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3267 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement HKL-2000 data collection HKL-2000 data reduction CNS phasing