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The Three-dimensional structure of the N-Acetylglucosamine-6- phosphate deacetylase from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O12 PDB ENTRY 1O12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8% PEG 20K (W/V), 8% PEG 550 MME (V/V), 0.1M HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.83 56.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.68 α = 90 b = 107.74 β = 90 c = 188.25 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 CCD ADSC CCD 2003-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 30 97.4 0.09 7.5 2.5 71574 1.5
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 2.07 94.3 0.41 2.36 2.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT PDB ENTRY 1O12 2.05 21.84 2 65440 3328 97.7 0.208 0.205 0.2046 0.26 0.2556 RANDOM 27.03
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] 0.027 -0.009 -0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.508 r_dihedral_angle_4_deg 18.276 r_dihedral_angle_3_deg 16.666 r_dihedral_angle_1_deg 6.641 r_scangle_it 3.773 r_scbond_it 2.473 r_angle_refined_deg 1.665 r_mcangle_it 1.546 r_mcbond_it 0.968 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.508 r_dihedral_angle_4_deg 18.276 r_dihedral_angle_3_deg 16.666 r_dihedral_angle_1_deg 6.641 r_scangle_it 3.773 r_scbond_it 2.473 r_angle_refined_deg 1.665 r_mcangle_it 1.546 r_mcbond_it 0.968 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.124 r_symmetry_hbond_refined 0.118 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5931 Nucleic Acid Atoms Solvent Atoms 620 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement AMoRE phasing