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Crystal analysis of the complex structure, E201A-cellotetraose, of endocellulase from pyrococcus horikoshii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZUM PDB ENTRY 2ZUM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 1.5M AMMONIUM PHOSPHATE, 0.1M MES BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.98 37.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.325 α = 90 b = 58.347 β = 109.61 c = 138.271 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 RIGAKU JUPITER 210 2008-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 SPring-8 BL38B1
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 1.99 50 95.1 0.072 12.1 3.4 79673
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 1.99 2.06 82.1 0.287 3.1
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 2ZUM 1.99 28.99 75684 3985 94.8 0.198 0.196 0.1979 0.248 0.2007 RANDOM 29.68
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] 0.21 0.13 -0.06 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.686 r_dihedral_angle_3_deg 16.314 r_dihedral_angle_4_deg 15.891 r_dihedral_angle_1_deg 7.033 r_scangle_it 3.579 r_scbond_it 2.635 r_angle_refined_deg 1.845 r_mcangle_it 1.814 r_mcbond_it 1.146 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.686 r_dihedral_angle_3_deg 16.314 r_dihedral_angle_4_deg 15.891 r_dihedral_angle_1_deg 7.033 r_scangle_it 3.579 r_scbond_it 2.635 r_angle_refined_deg 1.845 r_mcangle_it 1.814 r_mcbond_it 1.146 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.238 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.135 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 9201 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction DENZO data reduction SCALEPACK data scaling