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The Crystal Structure of LYN from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NMW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Citric acid pH3.5, 3.0M NaCl
Crystal Properties Matthews coefficient Solvent content 2.32 46.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.73 α = 90 b = 45.73 β = 90 c = 56.686 γ = 120
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 EIGER X 16M 2022-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.99999 SPring-8 BL41XU
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 1.3 39.603 99.7 0.078 19.2 9.6 16562
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 1.3 1.32 0.293
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.3 39.603 16529 806 99.668 0.157 0.1552 0.1532 0.1822 0.1812 14.955
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] -0.446 -0.223 -0.446 1.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.59 r_dihedral_angle_3_deg 11.098 r_dihedral_angle_1_deg 5.909 r_lrange_it 4.419 r_lrange_other 3.76 r_rigid_bond_restr 2.745 r_scangle_it 2.524 r_scangle_other 2.521 r_mcangle_other 2.37 r_mcangle_it 2.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.59 r_dihedral_angle_3_deg 11.098 r_dihedral_angle_1_deg 5.909 r_lrange_it 4.419 r_lrange_other 3.76 r_rigid_bond_restr 2.745 r_scangle_it 2.524 r_scangle_other 2.521 r_mcangle_other 2.37 r_mcangle_it 2.349 r_scbond_it 2.074 r_scbond_other 2.061 r_mcbond_it 1.606 r_mcbond_other 1.572 r_angle_refined_deg 1.569 r_angle_other_deg 1.421 r_symmetry_nbd_refined 0.232 r_nbd_other 0.225 r_symmetry_xyhbond_nbd_refined 0.216 r_symmetry_nbd_other 0.19 r_nbd_refined 0.181 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 506 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing