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Crystal structure of barley exohydrolaseI W434F mutant in complex with methyl 6-thio-beta-gentiobioside
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 64.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.609 α = 90 b = 100.609 β = 90 c = 180.38 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 1.89 87.87 99.7 0.12 36.8 24.2 70770
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 1.89 1.94 0.12
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3WLI 1.89 45.96 70770 3757 99.74 0.1309 0.1294 0.1584 0.1535 RANDOM 28.195
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] 0.63 0.63 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.238 r_dihedral_angle_4_deg 19.124 r_dihedral_angle_3_deg 13.632 r_dihedral_angle_1_deg 7.253 r_angle_refined_deg 2.122 r_angle_other_deg 1.817 r_chiral_restr 0.138 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.238 r_dihedral_angle_4_deg 19.124 r_dihedral_angle_3_deg 13.632 r_dihedral_angle_1_deg 7.253 r_angle_refined_deg 2.122 r_angle_other_deg 1.817 r_chiral_restr 0.138 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4568 Nucleic Acid Atoms Solvent Atoms 601 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing