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Crystal structures of catalytic site mutants of active domain 2 of thermostable chitinase from Pyrococcus furiosus complexed with chito-oligosaccharides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DSK PDB ENTRY 2DSK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 VAPOR DIFFUSION, HANGING DROP, pH6.0, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.21 61.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.005 α = 90 b = 91.985 β = 90 c = 107.499 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 CCD Bruker DIP-6040 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.8 30 83345
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 2DSK 1.8 29.49 78928 4147 99.54 0.1553 0.15432 0.1563 0.17394 0.1764 RANDOM 10.401
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.172 r_dihedral_angle_4_deg 23.206 r_dihedral_angle_3_deg 11.654 r_dihedral_angle_1_deg 5.661 r_scangle_it 3.356 r_scbond_it 1.992 r_angle_refined_deg 1.297 r_mcangle_it 1.198 r_mcbond_it 0.609 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.172 r_dihedral_angle_4_deg 23.206 r_dihedral_angle_3_deg 11.654 r_dihedral_angle_1_deg 5.661 r_scangle_it 3.356 r_scbond_it 1.992 r_angle_refined_deg 1.297 r_mcangle_it 1.198 r_mcbond_it 0.609 r_chiral_restr 0.094 r_bond_refined_d 0.011 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement