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Functional Analysis of Hyperthermophilic Endocellulase from the Archaeon Pyrococcus horikoshii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ECE PDB ENTRY 1ECE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 0.15M zinc acetate, 0.1M MES buffer pH 6.0, 40% (v/v) ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.31 46.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.15 α = 90 b = 77.15 β = 90 c = 161.105 γ = 90
Symmetry Space Group P 41 21 2
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 RIGAKU JUPITER 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.00000 SPring-8 BL38B1
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 1.95 50 98.4 13.5 36407 35824
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 1ECE 1.95 38.58 33956 1787 98.44 0.17398 0.17151 0.1715 0.2209 0.217 RANDOM 33.771
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 36.134 r_dihedral_angle_4_deg 16.339 r_dihedral_angle_3_deg 15.378 r_dihedral_angle_1_deg 7.108 r_scangle_it 4.054 r_scbond_it 2.837 r_angle_refined_deg 1.929 r_mcangle_it 1.762 r_mcbond_it 1.083 r_chiral_restr 0.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.134 r_dihedral_angle_4_deg 16.339 r_dihedral_angle_3_deg 15.378 r_dihedral_angle_1_deg 7.108 r_scangle_it 4.054 r_scbond_it 2.837 r_angle_refined_deg 1.929 r_mcangle_it 1.762 r_mcbond_it 1.083 r_chiral_restr 0.227 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 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 3081 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASES phasing