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Crystal structure of human myelin protein P2 at room temperature from joint X-ray and neutron refinement.
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WUT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 281 28% PEG 6000, 0.1 M citrate, pD 4.75
Crystal Properties Matthews coefficient Solvent content 2.82 56.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.952 α = 90 b = 57.952 β = 90 c = 100.79 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 neutron 292 AREA DETECTOR LADI III 2014-09-02 L LAUE 2 1 x-ray 293 IMAGE PLATE MAR scanner 345 mm plate 2016-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 NUCLEAR REACTOR ILL BEAMLINE LADI III 3.0-3.9 ILL LADI III 2 SEALED TUBE Xenocs GeniX 3D Cu HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 2 2 15 98.9 0.06 0.063 0.999 25.2 9.7 12464 27.66 1 2.4 40 60.1 0.189 6.1 4.2 4232 27.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2 2.06 0.431 0.513 0.849 3 3.2 1 2.4 2.53 0.304 2.8 2.2
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2 14.53 1.34 12443 1246 98.97 0.1596 0.1546 0.1562 0.2032 0.2046 18.85 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.4 40 4227 58.9 0.2995 0.2947 0.3412
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 17.656 f_angle_d 2.0852 f_chiral_restr 0.104 f_bond_d 0.0292 f_plane_restr 0.0129
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1048 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing