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X-ray structure of human A2ML1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other densities from EM map
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M Potassium phosphate dibasic, 10 % PEG 3350 pH 9.2
Crystal Properties Matthews coefficient Solvent content 4.92 75.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 320.15 α = 90 b = 320.15 β = 90 c = 321.94 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 2019-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9793 MAX IV BioMAX
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 4.276 211 99.4 0.301 0.998 8.75 58.7 43680 291.89
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 4.276 4.38 93.3 0.261
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 densities from EM map 4.4 49.37 1.33 40163 1846 99.82 0.2397 0.238 0.2385 0.2764 0.2748 342.83
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 13.0607 f_angle_d 0.8809 f_chiral_restr 0.0512 f_plane_restr 0.0074 f_bond_d 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21458 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 307
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing