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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 2.48 50.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.36 α = 90 b = 52.49 β = 105.942 c = 76.55 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 1.95 97.289 91.2 0.054 0.064 0.035 0.999 12.3 3.3 25683
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 1.95 2.241 71.9 0.769 0.93 0.516 0.528 1.7 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 1.95 97.289 25683 1268 45.236 0.19 0.186 0.1941 0.2674 0.2667 59.275
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] -0.092 -0.165 0.217 -0.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.766 r_dihedral_angle_3_deg 18.456 r_dihedral_angle_6_deg 15.49 r_lrange_other 12.508 r_lrange_it 12.501 r_dihedral_angle_1_deg 9.142 r_mcangle_it 7.863 r_mcangle_other 7.863 r_scangle_it 7.677 r_scangle_other 7.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.766 r_dihedral_angle_3_deg 18.456 r_dihedral_angle_6_deg 15.49 r_lrange_other 12.508 r_lrange_it 12.501 r_dihedral_angle_1_deg 9.142 r_mcangle_it 7.863 r_mcangle_other 7.863 r_scangle_it 7.677 r_scangle_other 7.676 r_mcbond_it 5.069 r_mcbond_other 5.065 r_scbond_it 4.888 r_scbond_other 4.888 r_angle_refined_deg 1.404 r_angle_other_deg 0.482 r_metal_ion_refined 0.252 r_nbd_refined 0.215 r_symmetry_nbd_other 0.203 r_xyhbond_nbd_refined 0.202 r_nbtor_refined 0.182 r_symmetry_nbd_refined 0.167 r_nbd_other 0.138 r_symmetry_xyhbond_nbd_refined 0.105 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.05 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4988 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing