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Vibrio cholerae family 3 glycoside hydrolase (NagZ) in complex with PUGNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 298 15% PEG 20000, 100mM Bis-Tris, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.734 α = 90 b = 67.85 β = 90 c = 96.894 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 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
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 1.7 55.56 99.3 0.061 27.2 7.1 35845 35787
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 1.7 1.79 95.5 0.167 8.4 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1TR9 1.7 55.56 35779 1783 99.14 0.17 0.168 0.1769 0.199 0.2063 RANDOM 8.485
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] -0.06 -0.44 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.772 r_dihedral_angle_3_deg 11.905 r_dihedral_angle_4_deg 11.768 r_dihedral_angle_1_deg 5.639 r_scangle_it 3.394 r_scbond_it 2.397 r_angle_refined_deg 1.298 r_mcangle_it 1.171 r_mcbond_it 1.137 r_angle_other_deg 0.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.772 r_dihedral_angle_3_deg 11.905 r_dihedral_angle_4_deg 11.768 r_dihedral_angle_1_deg 5.639 r_scangle_it 3.394 r_scbond_it 2.397 r_angle_refined_deg 1.298 r_mcangle_it 1.171 r_mcbond_it 1.137 r_angle_other_deg 0.905 r_symmetry_vdw_other 0.321 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.212 r_mcbond_other 0.203 r_nbd_other 0.2 r_nbtor_refined 0.174 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.132 r_nbtor_other 0.083 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2592 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction SCALA data scaling PHASER phasing