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Crystal structure of Pictet-Spenglerase AsKslB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 296.15 PEG400
Crystal Properties Matthews coefficient Solvent content 2.36 47.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.141 α = 90 b = 59.141 β = 90 c = 358.333 γ = 120
Symmetry Space Group P 65 2 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 PIXEL DECTRIS PILATUS3 6M 2020-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.987 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.6 50 99.6 0.121 0.123 0.021 0.808 4.6 36.3 12529
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 99.3 0.407 0.412 0.065 0.984 38.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.6 29.19 11351 621 95.95 0.20191 0.19942 0.206 0.24822 0.2526 RANDOM 32.421
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] 0.77 0.38 0.77 -2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.583 r_dihedral_angle_3_deg 15.646 r_dihedral_angle_1_deg 6.771 r_long_range_B_refined 6.295 r_long_range_B_other 6.294 r_scangle_other 4.51 r_mcangle_it 3.714 r_mcangle_other 3.714 r_scbond_it 2.861 r_scbond_other 2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.583 r_dihedral_angle_3_deg 15.646 r_dihedral_angle_1_deg 6.771 r_long_range_B_refined 6.295 r_long_range_B_other 6.294 r_scangle_other 4.51 r_mcangle_it 3.714 r_mcangle_other 3.714 r_scbond_it 2.861 r_scbond_other 2.86 r_mcbond_it 2.431 r_mcbond_other 2.427 r_angle_refined_deg 1.429 r_angle_other_deg 0.783 r_chiral_restr 0.076 r_gen_planes_other 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 2308 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling