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Structure of Phanerochaete chrysosporium cellobiohydrolase Cel7D (CBH58) in complex with cellobioimidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GPI PDB entry 1GPI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 TRIS-HCl, calcium chloride, PEG 5000, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.382 α = 90 b = 46.578 β = 102.58 c = 98.505 γ = 90
Symmetry Space Group C 1 2 1
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 QUANTUM 4 Toroidal mirror 2001-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 ESRF ID14-2
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 1.7 43 93.2 0.052 14 2.3 39785 39785
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 1.7 1.79 92.4 0.194 3.8 2685
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1GPI 1.7 36.27 37334 37334 2350 100 0.18108 0.17824 0.1843 0.22729 0.2356 RANDOM 17.761
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] 1.27 -0.61 -0.25 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.896 r_dihedral_angle_1_deg 6.044 r_scangle_it 5.472 r_mcangle_it 4.842 r_scbond_it 4.323 r_mcbond_it 4.126 r_angle_refined_deg 1.215 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.896 r_dihedral_angle_1_deg 6.044 r_scangle_it 5.472 r_mcangle_it 4.842 r_scbond_it 4.323 r_mcbond_it 4.126 r_angle_refined_deg 1.215 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.086 r_symmetry_hbond_refined 0.049 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3198 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing