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Structure of Phanerochaete chrysosporium cellobiohydrolase Cel7D (CBH58) in complex with lactose
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 42.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.947 α = 90 b = 46.7 β = 102.77 c = 99.124 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 1999-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9322 ESRF ID14-4
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 1.6 50 99.3 0.072 14.8 3.4 50272 50272
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 1.6 1.63 99.6 0.238 8.1 3286
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 1.61 39.22 47274 47274 2998 100 0.1605 0.15788 0.1638 0.20197 0.2048 RANDOM 22.962
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] 1.47 -0.94 -0.34 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.097 r_sphericity_free 10.552 r_sphericity_bonded 8.045 r_dihedral_angle_1_deg 6.681 r_scangle_it 5.972 r_scbond_it 4.634 r_mcangle_it 3.573 r_rigid_bond_restr 2.859 r_mcbond_it 2.68 r_angle_refined_deg 1.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.097 r_sphericity_free 10.552 r_sphericity_bonded 8.045 r_dihedral_angle_1_deg 6.681 r_scangle_it 5.972 r_scbond_it 4.634 r_mcangle_it 3.573 r_rigid_bond_restr 2.859 r_mcbond_it 2.68 r_angle_refined_deg 1.511 r_symmetry_hbond_refined 0.788 r_symmetry_vdw_refined 0.339 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.14 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3198 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing