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Crystal structure of Protein Arginine Deiminase 2 (100 uM 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 2.41 49.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.76 α = 90 b = 51.585 β = 105.43 c = 75.707 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 CCD MARMOSAIC 225 mm CCD vertical focusing mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
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 1.968 33.823 94.1 0.111 10.8 3.8 50413 18.34
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 1.968 0.388 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 1.968 33.823 1.35 50413 2527 93.94 0.1767 0.1745 0.172 0.2169 0.214 24.7048
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] -5.1983 -1.4574 6.1361 -0.9378
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.547 f_angle_d 1.296 f_chiral_restr 0.103 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5033 Nucleic Acid Atoms Solvent Atoms 547 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing