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Crystal structure of the human PAD2 protein bound to inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other internally determined apo structure of PAD2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293.15 0.1M Magnesium acetate, 50mM MES pH5.5, 9-16% 2-methyl 2, 4-pentane diol
Crystal Properties Matthews coefficient Solvent content 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.26 α = 90 b = 50.73 β = 105.077 c = 75.56 γ = 90
Symmetry Space Group C 1 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 EIGER2 X 9M 2018-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
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 1.64 97.659 93.6 0.054 0.064 0.035 0.999 13.2 3.3 61124
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 1.64 1.801 75.3 0.864 0.555 0.514 1.5 3.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.64 97.649 61123 2970 67.133 0.174 0.1721 0.2114 0.2028 26.335
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] -0.02 -0.016 0.039 -0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.361 r_dihedral_angle_3_deg 16.62 r_dihedral_angle_6_deg 16.588 r_lrange_it 8.109 r_lrange_other 8.014 r_dihedral_angle_1_deg 7.563 r_scangle_it 5.567 r_scangle_other 5.566 r_mcangle_it 3.976 r_mcangle_other 3.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.361 r_dihedral_angle_3_deg 16.62 r_dihedral_angle_6_deg 16.588 r_lrange_it 8.109 r_lrange_other 8.014 r_dihedral_angle_1_deg 7.563 r_scangle_it 5.567 r_scangle_other 5.566 r_mcangle_it 3.976 r_mcangle_other 3.976 r_scbond_it 3.578 r_scbond_other 3.577 r_mcbond_it 2.597 r_mcbond_other 2.597 r_angle_refined_deg 1.461 r_angle_other_deg 0.514 r_metal_ion_refined 0.319 r_xyhbond_nbd_refined 0.227 r_symmetry_xyhbond_nbd_refined 0.227 r_nbd_refined 0.218 r_nbd_other 0.204 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.179 r_symmetry_nbd_refined 0.17 r_xyhbond_nbd_other 0.129 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5038 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing