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Crystal Structure Of The N-Acetylglucosamine-6-Phosphate Deacetylase From Escherichia Coli K12 at 2.0 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other EXPERIMENTAL PHASES FROM AN IODINE SOAKED CRYSTAL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 293 sodium dihydrogenophosphate hydrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 4.00
Crystal Properties Matthews coefficient Solvent content 2.3 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.157 α = 90 b = 114.554 β = 90 c = 80.208 γ = 90
Symmetry Space Group P 21 21 2
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 MAR scanner 345 mm plate 1999-01-28 M SINGLE WAVELENGTH 2 1 x-ray M 3 1 x-ray M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 LNLS D03B-MX1
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 1,2,3 2 20 97.7 0.06 14.1 3.4 50702 2 35.8
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) 1,2,3 2 2.05 99.3 0.22 4.27 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 SIRAS THROUGHOUT EXPERIMENTAL PHASES FROM AN IODINE SOAKED CRYSTAL 2 20 50702 48144 2540 97.7 0.161 0.159 0.2047 0.199 0.235 RANDOM 17.92
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] 0.57 -0.96 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.751 r_scangle_it 4.607 r_scbond_it 2.837 r_angle_refined_deg 1.887 r_mcangle_it 1.845 r_angle_other_deg 1.593 r_mcbond_it 1.091 r_symmetry_vdw_other 0.32 r_symmetry_hbond_refined 0.308 r_symmetry_vdw_refined 0.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.751 r_scangle_it 4.607 r_scbond_it 2.837 r_angle_refined_deg 1.887 r_mcangle_it 1.845 r_angle_other_deg 1.593 r_mcbond_it 1.091 r_symmetry_vdw_other 0.32 r_symmetry_hbond_refined 0.308 r_symmetry_vdw_refined 0.272 r_nbd_other 0.249 r_nbd_refined 0.22 r_chiral_restr 0.202 r_xyhbond_nbd_refined 0.169 r_nbtor_other 0.091 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 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_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 5371 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SHELXD phasing SOLVE phasing RESOLVE phasing