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Structure of 3-keto-L-gulonate 6-phosphate decarboxylase E112D/T169A mutant with bound D-ribulose 5-phosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 273 16% PEG 5000 methyl ether, 100 mM BTP pH 7.0, 5 mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.785 α = 90 b = 41.906 β = 97.46 c = 91.225 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 2004-04-01 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 1.58 92 98.4 0.058 27.7 410568 63096
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) 1.58 1.64 89.8 0.335 3.5
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 1.58 91.29 58692 58962 3142 98.27 0.15967 0.15967 0.15792 0.171 0.19279 0.205 RANDOM 18.72
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] -1.32 -0.14 2.95 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.123 r_scangle_it 5.531 r_scbond_it 3.776 r_mcangle_it 2.568 r_angle_refined_deg 1.661 r_mcbond_it 1.642 r_angle_other_deg 0.865 r_symmetry_vdw_other 0.296 r_nbd_refined 0.27 r_nbd_other 0.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.123 r_scangle_it 5.531 r_scbond_it 3.776 r_mcangle_it 2.568 r_angle_refined_deg 1.661 r_mcbond_it 1.642 r_angle_other_deg 0.865 r_symmetry_vdw_other 0.296 r_nbd_refined 0.27 r_nbd_other 0.251 r_symmetry_hbond_refined 0.218 r_xyhbond_nbd_refined 0.172 r_symmetry_vdw_refined 0.166 r_chiral_restr 0.103 r_nbtor_other 0.082 r_bond_refined_d 0.018 r_metal_ion_refined 0.015 r_gen_planes_refined 0.007 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 3264 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing