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Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue of human O-GlcNAcase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30 % PEG 8000) AND 0.25 MICROLITER OF 40 % V/V GAMMA-BUTYROLACTONE TO A 1 PLUS MICROLITER DROP
Crystal Properties Matthews coefficient Solvent content 2.51 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.939 α = 90 b = 147.38 β = 90 c = 157.687 γ = 90
Symmetry Space Group I 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 157 CCD MARRESEARCH MIRROR 2005-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.25 20 100 0.11 7.7 25.4 65956 2
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 2.25 2.33 100 0.48 7.6 18.6
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 SAD THROUGHOUT 2.25 20 65296 659 99.9 0.169 0.169 0.1711 0.22 0.2603 RANDOM 14.66
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] 0.92 1.62 -2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.218 r_dihedral_angle_4_deg 20.703 r_dihedral_angle_3_deg 16.27 r_dihedral_angle_1_deg 6.373 r_scangle_it 5.034 r_scbond_it 3.436 r_mcangle_it 1.954 r_angle_refined_deg 1.47 r_mcbond_it 1.266 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.218 r_dihedral_angle_4_deg 20.703 r_dihedral_angle_3_deg 16.27 r_dihedral_angle_1_deg 6.373 r_scangle_it 5.034 r_scbond_it 3.436 r_mcangle_it 1.954 r_angle_refined_deg 1.47 r_mcbond_it 1.266 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.105 r_bond_refined_d 0.016 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 9240 Nucleic Acid Atoms Solvent Atoms 650 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing