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Crystal structure of cyanase from T. urticae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M Tris pH 7.5, 15% PEG6000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.074 α = 90 b = 81.611 β = 100.37 c = 136.466 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX300-HS 2016-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.8 40 99.9 0.069 0.069 0.102 0.05 22.5 4.1 38010 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 100 0.546 0.546 0.721 0.35 0.8 2 4.2
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 2IV1 2.8 40 36100 1886 99.63 0.22159 0.2206 0.2148 0.23997 0.2339 RANDOM 93.263
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] 1.11 7.24 -4.51 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.816 r_dihedral_angle_3_deg 15.39 r_dihedral_angle_4_deg 14.313 r_long_range_B_refined 8.655 r_long_range_B_other 8.655 r_dihedral_angle_1_deg 5.959 r_scangle_other 5.887 r_mcangle_it 5.214 r_mcangle_other 5.214 r_angle_other_deg 3.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.816 r_dihedral_angle_3_deg 15.39 r_dihedral_angle_4_deg 14.313 r_long_range_B_refined 8.655 r_long_range_B_other 8.655 r_dihedral_angle_1_deg 5.959 r_scangle_other 5.887 r_mcangle_it 5.214 r_mcangle_other 5.214 r_angle_other_deg 3.684 r_scbond_it 3.528 r_scbond_other 3.528 r_mcbond_it 3.212 r_mcbond_other 3.212 r_angle_refined_deg 1.668 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_other 0.008 r_gen_planes_refined 0.007 r_bond_other_d 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 10776 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing HKL-3000 phasing