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Crystal Structure of glucosamine 6-phosphate deaminase (NagB) with GlcN6P 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 2.93 58.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.92 α = 90 b = 82.48 β = 90 c = 135.28 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 MAR CCD 165 mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.00000 BSRF 3W1A
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 2.03 19.84 90.3 0.079 21.78 35757 -3 24.492
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 2.03 2.16 83.8 0.346 6.8
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 2.03 19.84 35757 1773 90.5 0.194 0.191 0.199 0.254 0.2586 RANDOM 5.14
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 -0.05 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.183 r_dihedral_angle_4_deg 19.463 r_dihedral_angle_3_deg 16.713 r_dihedral_angle_1_deg 7.538 r_scangle_it 3.266 r_angle_refined_deg 2.182 r_scbond_it 2.039 r_mcangle_it 0.903 r_mcbond_it 0.541 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.183 r_dihedral_angle_4_deg 19.463 r_dihedral_angle_3_deg 16.713 r_dihedral_angle_1_deg 7.538 r_scangle_it 3.266 r_angle_refined_deg 2.182 r_scbond_it 2.039 r_mcangle_it 0.903 r_mcbond_it 0.541 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.245 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.141 r_bond_refined_d 0.023 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3598 Nucleic Acid Atoms Solvent Atoms 460 Heterogen Atoms 60
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction