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D405N mutant of the CELLOBIOHYDROLASE CEL6A FROM HUMICOLA INSOLENS in complex with methyl-tetrathio-alpha-d-cellopentoside at 1.1 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OC5 PDB ENTRY 1OC5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 PROTEIN WAS CONCENTRATED TO 20 MG/ML IN WATER. CRYSTALLISATION IN 100MM MAGNESIUM ACETATE, 100MM ACETATE BUFFER AT PH 4.6. PRECIPITANT WAS 21% POLYETHYLENE GLYCOL 5000MME AND 5% DIMETHYLFORMAMIDE AS ADDITIVE.THE PROTEIN WAS INCUBATED WITH 1MM OF THE INHIBITOR PRIOR CRYSTALLISATION FOR AT LEAST 1 HOUR.
Crystal Properties Matthews coefficient Solvent content 4.05 38.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.504 α = 90 b = 60.148 β = 90 c = 97.207 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 MARRESEARCH 1999-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 1.1 20 96 0.053 23.7 4.3 120133
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 1.1 1.13 91.5 0.242 5.6 4.3
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 1OC5 1.11 20 120318 6359 94.5 0.106 0.105 0.124 0.124 0.1415 RANDOM 8.57
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] -0.31 0.28 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.071 r_dihedral_angle_4_deg 19.962 r_dihedral_angle_3_deg 10.94 r_dihedral_angle_1_deg 6.232 r_scangle_it 3.434 r_scbond_it 2.494 r_angle_refined_deg 1.907 r_angle_other_deg 1.861 r_mcangle_it 1.822 r_mcbond_it 1.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.071 r_dihedral_angle_4_deg 19.962 r_dihedral_angle_3_deg 10.94 r_dihedral_angle_1_deg 6.232 r_scangle_it 3.434 r_scbond_it 2.494 r_angle_refined_deg 1.907 r_angle_other_deg 1.861 r_mcangle_it 1.822 r_mcbond_it 1.269 r_nbd_other 0.274 r_symmetry_vdw_other 0.253 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.163 r_symmetry_hbond_refined 0.139 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.122 r_nbtor_other 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 2839 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling