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Crystal structure of H136A 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 2.18 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.116 α = 90 b = 42.059 β = 97.06 c = 91.07 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 IMAGE PLATE RIGAKU RAXIS IV 2003-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.9 91.29 99.2 0.065 26 36727 36727
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 91.8
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 (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 1.9 91.29 36727 34888 1839 99.29 0.1501 0.1501 0.14792 0.1604 0.19247 0.2066 RANDOM 19.972
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] -0.7 0.29 1.45 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.919 r_scangle_it 3.632 r_scbond_it 2.26 r_angle_other_deg 1.933 r_angle_refined_deg 1.528 r_mcangle_it 1.346 r_mcbond_it 0.773 r_symmetry_vdw_other 0.269 r_nbd_other 0.247 r_nbd_refined 0.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.919 r_scangle_it 3.632 r_scbond_it 2.26 r_angle_other_deg 1.933 r_angle_refined_deg 1.528 r_mcangle_it 1.346 r_mcbond_it 0.773 r_symmetry_vdw_other 0.269 r_nbd_other 0.247 r_nbd_refined 0.236 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.164 r_symmetry_vdw_refined 0.128 r_chiral_restr 0.106 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_metal_ion_refined 0.011 r_gen_planes_refined 0.006 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 3297 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling MOLREP phasing REFMAC refinement HKL-2000 data reduction