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Crystal Structure of glucosamine 6-phosphate deaminase (NagB) from S. mutans
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289 0.2M ammonium sulfate, 0.1M bis-Tris pH 5.5, 25%(w/v) PEG 3350, vapor diffusion, hanging drop, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.92 57.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54 α = 90 b = 82.17 β = 90 c = 134.91 γ = 90
Symmetry Space Group P 21 21 21
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 QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97564 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 1.5 45.13 79.3 0.069 18.32 76798 -3 24.622
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 1.5 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 1.6 45.13 76734 3865 96.67 0.178 0.177 0.1761 0.199 0.1997 RANDOM 12.575
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] 0.1 -0.07 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.956 r_dihedral_angle_4_deg 14.426 r_dihedral_angle_3_deg 12.123 r_dihedral_angle_1_deg 6.259 r_scangle_it 3.741 r_scbond_it 2.354 r_angle_refined_deg 1.455 r_mcangle_it 1.182 r_mcbond_it 0.657 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.956 r_dihedral_angle_4_deg 14.426 r_dihedral_angle_3_deg 12.123 r_dihedral_angle_1_deg 6.259 r_scangle_it 3.741 r_scbond_it 2.354 r_angle_refined_deg 1.455 r_mcangle_it 1.182 r_mcbond_it 0.657 r_nbtor_refined 0.314 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.203 r_chiral_restr 0.183 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.122 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3564 Nucleic Acid Atoms Solvent Atoms 663 Heterogen Atoms 30
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction