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CRYSTAL STRUCTURE ANALYSIS OF PLANT EXOHYDROLASE IN COMPLEX WITH METHYL 2-THIO-BETA-SOPHOROSIDE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IEQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 75MM HEPES-NAOH PH7.0, 1.2% PEG 400,
1.7M AMMONIUM SULPHATE , VAPOR DIFFUSION, HANGING DROP,
TEMPERATURE 277K
Crystal Properties Matthews coefficient Solvent content 3.63 66.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.311 α = 90 b = 100.311 β = 90 c = 182.153 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) R Sym 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 1.68 48.36 99.7 0.076 0.074 39.19 29.2 101119 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.78 99.3 0.76 0.75 4 28
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 1IEQ 1.68 46.13 101119 5311 99.91 0.13347 0.1321 0.1421 0.15902 0.1705 RANDOM 21.527
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] -0.02 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.549 r_dihedral_angle_4_deg 17.169 r_dihedral_angle_3_deg 12.974 r_long_range_B_refined 7.425 r_dihedral_angle_1_deg 6.915 r_long_range_B_other 6.858 r_scangle_other 4.013 r_scbond_it 2.843 r_scbond_other 2.843 r_angle_refined_deg 2.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.549 r_dihedral_angle_4_deg 17.169 r_dihedral_angle_3_deg 12.974 r_long_range_B_refined 7.425 r_dihedral_angle_1_deg 6.915 r_long_range_B_other 6.858 r_scangle_other 4.013 r_scbond_it 2.843 r_scbond_other 2.843 r_angle_refined_deg 2.282 r_angle_other_deg 1.907 r_mcangle_it 1.891 r_mcangle_other 1.891 r_mcbond_it 1.28 r_mcbond_other 1.28 r_chiral_restr 0.126 r_bond_refined_d 0.02 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4576 Nucleic Acid Atoms Solvent Atoms 1003 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing