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Crystal analysis of the complex structure, Y299F-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 37.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.164 α = 90 b = 58.528 β = 109.24 c = 138.317 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 Bruker DIP-6040 2009-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU SPring-8 BL44XU
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 1.65 50 94.9 0.064 25.1 3.3 139746
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 1.65 1.68 84.8 0.308 2.6
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 1.65 33.67 131973 6964 94.8 0.189 0.187 0.1839 0.227 0.222 RANDOM 25.43
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] 0.01 -0.02 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.515 r_dihedral_angle_4_deg 15.84 r_dihedral_angle_3_deg 14.784 r_dihedral_angle_1_deg 6.75 r_scangle_it 4.677 r_scbond_it 3.21 r_mcangle_it 2.277 r_angle_refined_deg 2.085 r_mcbond_it 1.403 r_chiral_restr 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.515 r_dihedral_angle_4_deg 15.84 r_dihedral_angle_3_deg 14.784 r_dihedral_angle_1_deg 6.75 r_scangle_it 4.677 r_scbond_it 3.21 r_mcangle_it 2.277 r_angle_refined_deg 2.085 r_mcbond_it 1.403 r_chiral_restr 0.156 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 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 9210 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction DENZO data reduction SCALEPACK data scaling