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Crystal structure of the oligomeric state of the extracellular domain of human myelin protein zero(MPZ/P0)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NEU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 100 mM Tris-HCl, 300 mM magnesium-formate
Crystal Properties Matthews coefficient Solvent content 3.16 61.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.579 α = 90 b = 88.579 β = 90 c = 88.988 γ = 90
Symmetry Space Group I 4 2 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 EIGER X 9M 2020-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.09 44.49 100 0.141 0.028 0.998 13.9 26.8 10861 49.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.14 99.5 3.297 0.634 0.815 1.1 27.4
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 1NEU 2.09 36.27 1.33 10844 501 99.81 0.2174 0.2167 0.2212 0.2319 0.2326 52.75
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 8.5501 f_angle_d 0.6959 f_chiral_restr 0.0524 f_plane_restr 0.0061 f_bond_d 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 982 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing