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The Crystal Structure of LCC6-Active from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M (NH4)2SO4, 0.1M Mes pH6.5, 30% w/v Polyethylene glycol Monomethyl ether 5,000
Crystal Properties Matthews coefficient Solvent content 2.1 41.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.611 α = 90 b = 74.69 β = 90 c = 157.453 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 PIXEL DECTRIS EIGER X 16M 2024-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979191 SSRF BL10U2
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 2.05 42.98 99.9 0.194 10.5 10 30250
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 2.05 2.11 0.979
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7vve 2.05 42.979 30188 1489 99.868 0.152 0.1496 0.1639 0.2018 0.2129 20.111
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] -0.986 -0.016 1.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.53 r_dihedral_angle_3_deg 14.01 r_dihedral_angle_1_deg 6.745 r_lrange_it 5.608 r_dihedral_angle_2_deg 5.425 r_lrange_other 5.295 r_scangle_it 3.746 r_scangle_other 3.745 r_scbond_it 2.469 r_scbond_other 2.468
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.53 r_dihedral_angle_3_deg 14.01 r_dihedral_angle_1_deg 6.745 r_lrange_it 5.608 r_dihedral_angle_2_deg 5.425 r_lrange_other 5.295 r_scangle_it 3.746 r_scangle_other 3.745 r_scbond_it 2.469 r_scbond_other 2.468 r_mcangle_it 2.299 r_mcangle_other 2.298 r_mcbond_it 1.524 r_mcbond_other 1.523 r_angle_refined_deg 1.336 r_angle_other_deg 0.451 r_xyhbond_nbd_refined 0.232 r_symmetry_xyhbond_nbd_refined 0.231 r_nbd_refined 0.215 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.178 r_nbd_other 0.172 r_symmetry_nbd_refined 0.154 r_ncsr_local_group_1 0.085 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3840 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing