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The FERM domain of Human EPB41L3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HE7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 0.15 M ammonium nitrate, 0.1 M MES, 5% (v/v) ethylene glycol, 5% (w/v) PEG 2000, 5% (w/v) PEG 3350, 5% (w/v) PEG 4000, 5% (w/v) PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 2.27 45.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.915 α = 90 b = 78.687 β = 90 c = 98.981 γ = 90
Symmetry Space Group P 21 21 21
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 2018-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 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 1.45 78.69 100 0.066 0.079 0.043 0.944 13.5 6.1 54827
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 1.45 1.48 100 1.536 1.896 1.098 0.401 1.3 5.4
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 (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 THROUGHOUT 2HE7 1.45 61.59 52770 1984 99.99 0.15562 0.15393 0.1636 0.19994 0.2037 RANDOM 25.261
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] 0.66 -0.04 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.935 r_dihedral_angle_4_deg 18.946 r_dihedral_angle_3_deg 13.645 r_dihedral_angle_1_deg 6.669 r_scangle_other 5.683 r_long_range_B_refined 5.256 r_long_range_B_other 5.242 r_scbond_it 4.539 r_scbond_other 4.536 r_mcangle_it 3.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.935 r_dihedral_angle_4_deg 18.946 r_dihedral_angle_3_deg 13.645 r_dihedral_angle_1_deg 6.669 r_scangle_other 5.683 r_long_range_B_refined 5.256 r_long_range_B_other 5.242 r_scbond_it 4.539 r_scbond_other 4.536 r_mcangle_it 3.957 r_mcangle_other 3.956 r_mcbond_other 3.404 r_mcbond_it 3.403 r_rigid_bond_restr 3.032 r_angle_refined_deg 1.695 r_angle_other_deg 1.459 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2334 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing