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Crystal structure of the human PAD2 protein bound to small molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Internal apo structure
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 2.49 50.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.71 α = 90 b = 52.78 β = 105.709 c = 76.59 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 2.003 97.088 92.2 0.038 0.045 0.025 0.999 16.3 3.3 26935
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 2.003 2.276 75.5 0.759 0.903 0.483 0.617 1.7 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.003 97.088 26935 1358 51.213 0.189 0.1857 0.195 0.2575 0.2629 59.135
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] -0.08 -0.205 0.259 -0.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.487 r_dihedral_angle_2_deg 18.017 r_dihedral_angle_6_deg 16.064 r_lrange_it 12.552 r_lrange_other 12.551 r_dihedral_angle_1_deg 9.209 r_scangle_it 8.262 r_scangle_other 8.26 r_mcangle_it 8.1 r_mcangle_other 8.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.487 r_dihedral_angle_2_deg 18.017 r_dihedral_angle_6_deg 16.064 r_lrange_it 12.552 r_lrange_other 12.551 r_dihedral_angle_1_deg 9.209 r_scangle_it 8.262 r_scangle_other 8.26 r_mcangle_it 8.1 r_mcangle_other 8.099 r_mcbond_it 5.48 r_mcbond_other 5.471 r_scbond_it 5.426 r_scbond_other 5.425 r_angle_refined_deg 1.51 r_angle_other_deg 0.516 r_xyhbond_nbd_refined 0.23 r_nbd_refined 0.224 r_symmetry_nbd_other 0.208 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.174 r_nbd_other 0.171 r_symmetry_nbd_refined 0.167 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4805 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing