☰ Navigation Tabs
Covalent glycosyl-enzyme intermediate of Hypocrea jecorina Cel7a E217Q mutant trapped using DNP-2-deoxy-2-fluoro-cellotrioside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CEL PDB ENTRY 7CEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 PROTEIN FIRST INCUBATED WITH 80 UM 2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-BETA-CELLOTRIOSIDE (DNP-2F-G3)4 IN 10 MM SODIUM MES, PH 6.0. ALIQUOTS WERE TAKEN AT REGULAR TIME INTERVALS AND CONCENTRATED FOR CRYSTALLISATION IN THE PRESENCE OF 1 MM FRESH DNP-2F-G3 ADDED TO THE CRYSTALLISATION DROPS. CRYSTALLISATION CONDITION: 0.1 M MES (PH 6.0), 20% MONOMETHYL ETHER PEG 5000, 0.01 M COCL2, 12% GLYCEROL.
Crystal Properties Matthews coefficient Solvent content 1.96 37.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.93 α = 90 b = 83.29 β = 90 c = 110.76 γ = 90
Symmetry Space Group I 2 2 2
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 ADSC CCD 1999-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.32 66.6 84175
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 7CEL 1.32 66.57 84175 4418 98.47 0.16774 0.16675 0.1658 0.18673 0.1847 RANDOM 11.508
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] -0.69 0.7 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.899 r_dihedral_angle_4_deg 16.622 r_dihedral_angle_3_deg 11.315 r_dihedral_angle_1_deg 6.165 r_angle_refined_deg 1.271 r_chiral_restr 0.086 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.899 r_dihedral_angle_4_deg 16.622 r_dihedral_angle_3_deg 11.315 r_dihedral_angle_1_deg 6.165 r_angle_refined_deg 1.271 r_chiral_restr 0.086 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 3224 Nucleic Acid Atoms Solvent Atoms 618 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling