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Paraplegin N-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 10mM NaCitrate, 15% Peg8k with seeds from 0.17M Ammonium sulfate, 25.5% PEG 4K, 15% glycerol
Crystal Properties Matthews coefficient Solvent content 2.26 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.393 α = 90 b = 63.844 β = 90 c = 99.813 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 XE 16M 2019-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979515 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.99 49.96 99.89 0.999 11.7 7.2 12698 42.56
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 1.99 2.01 62.9 0.664 8.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.99 49.956 12698 170 99.89 0.24 0.2386 0.239 0.2961 0.2608 64.309
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] 0.253 -0.309 0.056
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 16.94 r_lrange_it 16.932 r_dihedral_angle_6_deg 15.109 r_dihedral_angle_3_deg 14.288 r_scangle_it 8.146 r_scangle_other 8.145 r_mcangle_it 6.516 r_mcangle_other 6.512 r_dihedral_angle_1_deg 6.459 r_scbond_it 5.143
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 16.94 r_lrange_it 16.932 r_dihedral_angle_6_deg 15.109 r_dihedral_angle_3_deg 14.288 r_scangle_it 8.146 r_scangle_other 8.145 r_mcangle_it 6.516 r_mcangle_other 6.512 r_dihedral_angle_1_deg 6.459 r_scbond_it 5.143 r_scbond_other 5.141 r_mcbond_it 4.487 r_mcbond_other 4.487 r_dihedral_angle_2_deg 4.08 r_angle_refined_deg 1.455 r_angle_other_deg 0.493 r_nbd_refined 0.24 r_xyhbond_nbd_refined 0.24 r_symmetry_nbd_other 0.209 r_symmetry_xyhbond_nbd_refined 0.192 r_nbtor_refined 0.19 r_nbd_other 0.163 r_symmetry_nbd_refined 0.162 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.062 r_symmetry_xyhbond_nbd_other 0.021 r_xyhbond_nbd_other 0.012 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1365 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing