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Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound xylitol 5-phosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 298 15% 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 = 123.182 α = 90 b = 41.727 β = 95.87 c = 92.125 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 ADSC QUANTUM 4 2003-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.987 APS 14-BM-C
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 1.695 100 95.4 27.8 49427 2.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.695 1.75 82.8 5.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.695 91.29 49427 47189 2538 95.2 0.1735 0.17177 0.20656 0.2296 RANDOM 20.917
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] -1.16 0.45 1.14 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.402 r_scangle_it 5.259 r_scbond_it 3.642 r_mcangle_it 2.726 r_mcbond_it 1.783 r_angle_refined_deg 1.701 r_angle_other_deg 1.32 r_symmetry_vdw_other 0.294 r_nbd_other 0.246 r_nbd_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.402 r_scangle_it 5.259 r_scbond_it 3.642 r_mcangle_it 2.726 r_mcbond_it 1.783 r_angle_refined_deg 1.701 r_angle_other_deg 1.32 r_symmetry_vdw_other 0.294 r_nbd_other 0.246 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.192 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.122 r_nbtor_other 0.085 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 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 3276 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction CNS phasing