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Structure of Phanerochaete chrysosporium cellobiohydrolase Cel7D (CBH58) in complex with cellobiose
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 2.2 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.414 α = 90 b = 46.842 β = 102.99 c = 99.488 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 1999-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9370 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 1.7 50 99.6 0.098 11 4.3 43328 43328
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 1.73 93.1 0.321 5.8 2867
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 (All) 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 40 40782 40782 2541 100 0.172 0.16125 0.15879 0.1754 0.19866 0.2083 RANDOM 20.816
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] 2.53 -0.74 -1.17 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.152 r_sphericity_free 6.634 r_scangle_it 6.12 r_dihedral_angle_1_deg 5.299 r_sphericity_bonded 4.677 r_scbond_it 4.357 r_mcangle_it 3.204 r_rigid_bond_restr 2.599 r_mcbond_it 2.125 r_angle_refined_deg 2.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.152 r_sphericity_free 6.634 r_scangle_it 6.12 r_dihedral_angle_1_deg 5.299 r_sphericity_bonded 4.677 r_scbond_it 4.357 r_mcangle_it 3.204 r_rigid_bond_restr 2.599 r_mcbond_it 2.125 r_angle_refined_deg 2.062 r_angle_other_deg 0.983 r_nbtor_other 0.694 r_symmetry_hbond_refined 0.606 r_xyhbond_nbd_refined 0.362 r_symmetry_vdw_refined 0.357 r_nbd_refined 0.35 r_symmetry_vdw_other 0.301 r_nbd_other 0.211 r_chiral_restr 0.135 r_xyhbond_nbd_other 0.053 r_bond_refined_d 0.026 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3198 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing