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Structure of 3-keto-L-gulonate 6-phosphate decarboxylase E112D/R139V/T169A mutant with bound D-ribulose 5-phosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 16% PEG 5000 methyl ether, 100 mM BTP, 5 mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123 α = 90 b = 41.831 β = 97.47 c = 91.068 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 1.8 90 99.8 0.081 17.9 746805 42532 2
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 1.86 100 0.24 4.3
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 1.81 90 40307 40307 2143 99.54 0.14249 0.14249 0.14063 0.1431 0.17762 0.1785 RANDOM 14.374
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] -1.14 -0.22 2.07 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.237 r_scangle_it 4.668 r_scbond_it 2.99 r_mcangle_it 1.619 r_angle_refined_deg 1.547 r_mcbond_it 0.894 r_angle_other_deg 0.865 r_symmetry_vdw_other 0.285 r_nbd_refined 0.27 r_nbd_other 0.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.237 r_scangle_it 4.668 r_scbond_it 2.99 r_mcangle_it 1.619 r_angle_refined_deg 1.547 r_mcbond_it 0.894 r_angle_other_deg 0.865 r_symmetry_vdw_other 0.285 r_nbd_refined 0.27 r_nbd_other 0.249 r_xyhbond_nbd_refined 0.217 r_symmetry_hbond_refined 0.172 r_chiral_restr 0.105 r_symmetry_vdw_refined 0.102 r_nbtor_other 0.08 r_bond_refined_d 0.017 r_metal_ion_refined 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 r_bond_other_d 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 3256 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing