☰ Navigation Tabs
Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue of human O-GlcNAcase in complex with PUGNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CBI PDB ENTRY 2CBI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 30 % PEG 8000) AND 0.25 MICROLITERS OF 40 % V/V GAMMA-BUTYROLACTONE ADDED TO A 1 PLUS 1 MICROLITER DROP
Crystal Properties Matthews coefficient Solvent content 2.69 53.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.613 α = 90 b = 145.745 β = 90 c = 152.8 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 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2005-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 2.35 20 93.7 0.08 15.8 3.9 56462 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 2.35 2.43 96 0.61 2.6 3.6
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 PDB ENTRY 2CBI 2.35 20 55837 562 93.5 0.194 0.193 0.1923 0.248 0.2455 RANDOM 42.28
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] 0.89 1.21 -2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.814 r_dihedral_angle_4_deg 19.39 r_dihedral_angle_3_deg 17.001 r_dihedral_angle_1_deg 6.514 r_scangle_it 5.902 r_scbond_it 4.135 r_mcangle_it 2.324 r_mcbond_it 1.51 r_angle_refined_deg 1.366 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.814 r_dihedral_angle_4_deg 19.39 r_dihedral_angle_3_deg 17.001 r_dihedral_angle_1_deg 6.514 r_scangle_it 5.902 r_scbond_it 4.135 r_mcangle_it 2.324 r_mcbond_it 1.51 r_angle_refined_deg 1.366 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.152 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 9257 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing