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Crystal structure of barley exohydrolaseI W434F in complex with 4'-nitrophenyl thiolaminaribioside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 1.7 M ammonium sulfate, 75 mM HEPES-NaOH buffer, pH 7, containing 7.5 mM sodium acetate and 1.2% (w/v) PEG 400
Crystal Properties Matthews coefficient Solvent content 3.47 64.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.774 α = 90 b = 100.774 β = 90 c = 180.169 γ = 90
Symmetry Space Group P 43 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 ADSC QUANTUM 210r COLLIMATING MIRROR 2012-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
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 1.76 87.95 99.9 0.119 36.5 13.7 87843
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 1.76 1.8 0.119
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 3WLI 1.76 45.96 87843 4631 99.87 0.1412 0.1397 0.149 0.1689 0.1787 RANDOM 25.221
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] 0.15 0.15 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.181 r_dihedral_angle_4_deg 16.059 r_dihedral_angle_3_deg 13.33 r_dihedral_angle_1_deg 8.319 r_angle_refined_deg 2.617 r_angle_other_deg 1.856 r_chiral_restr 0.166 r_bond_refined_d 0.027 r_gen_planes_refined 0.012 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.181 r_dihedral_angle_4_deg 16.059 r_dihedral_angle_3_deg 13.33 r_dihedral_angle_1_deg 8.319 r_angle_refined_deg 2.617 r_angle_other_deg 1.856 r_chiral_restr 0.166 r_bond_refined_d 0.027 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4568 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 206
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing