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Crystal structure of LnzB (Streptomyces spp. )
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 8 298 0.4 M Sodium phosphate monobasic, 1.6 M Potassium phosphate dibasic, 0.2 M NaCl and 0.1 M Imidazole, pH8.0
Crystal Properties Matthews coefficient Solvent content 2.6 52.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.621 α = 90 b = 162.475 β = 90 c = 59.032 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS 300K 2024-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CAMD BEAMLINE GCPCC 0.987 CAMD GCPCC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.14 81.24 91.7 0.998 12.9 10.2 52784 30.1846899792
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.26 0.917
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.30000255522 49.3154042357 1.32812535602 44525 1694 94.9866666667 0.207769246878 0.206399944253 0.2114 0.241530762396 0.2449 35.8203812679
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.5966918328 f_angle_d 1.26977843464 f_chiral_restr 0.0488569194111 f_bond_d 0.00876234701214 f_plane_restr 0.00836545063145
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6674 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling PHASER phasing