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Crystal structure of cyanase from the thermophilic fungus Thermomyces lanuginosus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 2% (w/v) Tacsimate (pH 8.0), 0.1 M Tris (pH 8.5), and 16% (w/v) polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.42 49.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.368 α = 90 b = 157.639 β = 90 c = 163.871 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2016-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97856 APS 24-ID-E
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 2.2 50 99.9 0.096 15 4.4 99692
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 2.2 2.28 99.5 0.381 4.3
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 1dw9 2.2 45.36 94642 4976 99.67 0.15679 0.15441 0.1677 0.20182 0.2086 RANDOM 25.645
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] -0.05 0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.562 r_dihedral_angle_3_deg 16.048 r_dihedral_angle_4_deg 11.432 r_long_range_B_refined 8.011 r_long_range_B_other 8.011 r_dihedral_angle_1_deg 6.487 r_scangle_other 5.161 r_mcangle_it 3.729 r_mcangle_other 3.729 r_scbond_it 3.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.562 r_dihedral_angle_3_deg 16.048 r_dihedral_angle_4_deg 11.432 r_long_range_B_refined 8.011 r_long_range_B_other 8.011 r_dihedral_angle_1_deg 6.487 r_scangle_other 5.161 r_mcangle_it 3.729 r_mcangle_other 3.729 r_scbond_it 3.296 r_scbond_other 3.287 r_mcbond_it 2.353 r_mcbond_other 2.353 r_angle_refined_deg 1.931 r_angle_other_deg 1.073 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 12520 Nucleic Acid Atoms Solvent Atoms 798 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing