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Crystal structure of Peptidyl Arginine Deiminase Type III (PADI3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Sodium HEPES + MOPS (acid)
Ethylene glycols
PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.75 55.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.023 α = 90 b = 115.023 β = 90 c = 328.487 γ = 120
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 EIGER X 16M 2017-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953694 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.8 49.24 100 0.132 0.993 8 18.6 21054 66.14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 100 2.16 0.334 0.8 17.5
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2DEW 2.8 49.24 21010 1032 99.79 0.2363 0.2344 0.2361 0.2735 0.2785 72.07
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.3143 f_angle_d 0.7759 f_chiral_restr 0.0519 f_plane_restr 0.0081 f_bond_d 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4253 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose phenix.refine refinement PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing Coot model building