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The high resolution structure of the FERM domain of human FERMT2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XPY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.1M HEPES pH 7.0, 1.4M sodium citrate tribasic
Crystal Properties Matthews coefficient Solvent content 3.45 64.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.172 α = 90 b = 145.172 β = 90 c = 59.633 γ = 120
Symmetry Space Group P 32 2 1
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 6M 2019-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.6 72.7 100 0.277 0.28 0.071 0.999 11 31.1 95151
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 99.7 5.732 5.965 1.638 0.732 1 25.4
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 5XPY 1.6 72.7 94810 1874 99.707 0.181 0.1807 0.19 0.2037 0.2121 29.736
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] 0.782 0.391 0.782 -2.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.234 r_dihedral_angle_4_deg 21.29 r_dihedral_angle_3_deg 14.463 r_dihedral_angle_1_deg 8.322 r_lrange_it 7.299 r_lrange_other 7.246 r_scangle_it 4.947 r_scangle_other 4.946 r_mcangle_it 3.834 r_mcangle_other 3.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.234 r_dihedral_angle_4_deg 21.29 r_dihedral_angle_3_deg 14.463 r_dihedral_angle_1_deg 8.322 r_lrange_it 7.299 r_lrange_other 7.246 r_scangle_it 4.947 r_scangle_other 4.946 r_mcangle_it 3.834 r_mcangle_other 3.833 r_scbond_it 3.044 r_scbond_other 3.026 r_mcbond_other 2.377 r_mcbond_it 2.376 r_angle_other_deg 2.286 r_angle_refined_deg 1.428 r_symmetry_xyhbond_nbd_other 0.459 r_nbd_refined 0.27 r_symmetry_nbd_refined 0.256 r_nbd_other 0.253 r_symmetry_nbd_other 0.224 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.141 r_chiral_restr 0.074 r_symmetry_nbtor_other 0.066 r_bond_other_d 0.034 r_gen_planes_other 0.01 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3694 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing