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Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-PUGNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OXN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 13% PEG 20,000, 10% glycerol, 100mM Bis-Tris pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.38 48.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.98 α = 90 b = 86.44 β = 90 c = 86.44 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++ 2008-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R 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 2.4 61.08 99.5 0.1 6.7 2.97 14609 14482
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 2.4 2.53 100 0.49 2.2 3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2OXN 2.4 61.08 15335 13755 727 99.14 0.2125 0.20937 0.27174 0.2406 RANDOM 26.499
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 -1.32 1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.705 r_dihedral_angle_4_deg 19.779 r_dihedral_angle_3_deg 17.257 r_dihedral_angle_1_deg 5.893 r_scangle_it 2.499 r_scbond_it 1.461 r_angle_refined_deg 1.311 r_mcangle_it 0.991 r_angle_other_deg 0.632 r_mcbond_it 0.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.705 r_dihedral_angle_4_deg 19.779 r_dihedral_angle_3_deg 17.257 r_dihedral_angle_1_deg 5.893 r_scangle_it 2.499 r_scbond_it 1.461 r_angle_refined_deg 1.311 r_mcangle_it 0.991 r_angle_other_deg 0.632 r_mcbond_it 0.523 r_mcbond_other 0.091 r_chiral_restr 0.065 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2512 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 30
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling