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Crystal structure of Protein Arginine Deiminase 2 (F221/222A, 10 mM Ca2+)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N25 PDB ENTRY 4N25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 10% MPD, 10% ethanol, 50 mM MES, pH 5.6, 20 mM magnesium chloride, 1 mM spermidine, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.47 50.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.93 α = 90 b = 52.18 β = 105.21 c = 75.82 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 ADSC QUANTUM 315r Rh coated flat mirror 2012-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.2836 SSRL BL7-1
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 3.02 48.955 98.7 0.083 17 4.1 13566 35.33
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 3.02 0.335 4.5
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 4N25 3.022 48.955 1.36 13566 659 88.32 0.2467 0.2453 0.2425 0.2728 0.2705 36.3383
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] -0.0644 -2.0613 -1.2032 1.2676
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.014 f_angle_d 0.959 f_chiral_restr 0.069 f_bond_d 0.021 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4988 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data scaling HKL-2000 data reduction HKL-2000 data scaling PHASER phasing