☰ Navigation Tabs
LXG-associated alpha-helical protein D2 (LapD2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SAD model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 0.2M lithium sulfate, 0.1M Tris-HCl, pH 8.0, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.96 58.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.59 α = 90 b = 45.59 β = 90 c = 298.44 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 PILATUS3 X 6M 2021-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97926 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 42.6 99.3 0.078 0.999 12.9 11.1 34956 54.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 90.6 2.12 0.474 0.8 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 SAD model 2.2 39.48 3.83 34776 1606 98.77 0.2373 0.2333 0.2346 0.2667 0.2694 76.18
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 4.3593 f_angle_d 0.7329 f_chiral_restr 0.0373 f_bond_d 0.0054 f_plane_restr 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3707 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement SBC-Collect data collection xia2 data reduction xia2 data scaling Aimless data scaling HKL-3000 phasing MOLREP phasing