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Crystal structure of Protein Arginine Deiminase 2 (D177A, 0 mM Ca2+)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N20 PDB ENTRY 4N20
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 10-20% MPD, 50 mM MES, pH 5.6, 0.12 M sodium acetate, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.46 49.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.312 α = 90 b = 52.035 β = 105.31 c = 76.072 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 CCD MARMOSAIC 300 mm CCD beryllium lenses 2013-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9787 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 40.633 99.1 0.083 18.6 4.1 69484 20.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 100 0.65 2
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 4N20 1.808 40.633 1.36 69484 3259 98.99 0.1742 0.1722 0.168 0.2109 0.2068 27.9177
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] -5.0744 -2.3117 6.0272 -0.9528
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.835 f_angle_d 1.263 f_chiral_restr 0.109 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5033 Nucleic Acid Atoms Solvent Atoms 675 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing