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Crystal structure of E112Q mutant of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-threonohydroxamate 4-phosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 293 16% PEG 5000 methyl ether, 100 mM BTP pH 7.0, 5 mM MgCl2, Microbatch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.756 α = 90 b = 41.849 β = 97.24 c = 91.009 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 2003-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.961 APS 19-ID
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 1.8 91.29 98.3 0.66 25.7 42041 42041
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) 1.8 1.86 98.3 0.24 6.6
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 (All) 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 1.8 91.29 42041 39925 2116 98.16 0.15759 0.15759 0.15558 0.168 0.19649 0.2087 RANDOM 15.634
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] -0.84 -0.05 1.34 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.041 r_scangle_it 4.004 r_scbond_it 2.514 r_mcangle_it 1.406 r_angle_refined_deg 1.384 r_angle_other_deg 0.817 r_mcbond_it 0.747 r_symmetry_vdw_other 0.287 r_nbd_other 0.248 r_nbd_refined 0.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.041 r_scangle_it 4.004 r_scbond_it 2.514 r_mcangle_it 1.406 r_angle_refined_deg 1.384 r_angle_other_deg 0.817 r_mcbond_it 0.747 r_symmetry_vdw_other 0.287 r_nbd_other 0.248 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.088 r_symmetry_vdw_refined 0.084 r_nbtor_other 0.081 r_metal_ion_refined 0.036 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3270 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling MOLREP phasing REFMAC refinement HKL-2000 data reduction