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Crystal structure of the stable degradation fragment of human plakophilin 2 isoform a (PKP2a) C752R variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XM9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 reservoir: 22% (w/v) PEG 3350, 75 M malonic acid pH 7.0, protein: 5 mg/mL in 20 mM HEPES, NaOH pH 7.5, 0.1 M NaCl, 3 mM DTT, mix 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.09 41.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.35 α = 90 b = 63.038 β = 90 c = 74.953 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX-225 2009-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.55 35 99.4 32554 32363 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.59 98.3 2.87
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1XM9 1.55 33.42 -3 32554 30744 1619 100 0.15994 0.15994 0.15822 0.1525 0.19231 0.1854 RANDOM 13.662
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] -0.47 -0.31 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.115 r_dihedral_angle_4_deg 17.898 r_dihedral_angle_3_deg 12.853 r_dihedral_angle_1_deg 4.922 r_scangle_it 4.466 r_scbond_it 2.754 r_angle_refined_deg 1.595 r_mcangle_it 1.585 r_mcbond_it 0.922 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.115 r_dihedral_angle_4_deg 17.898 r_dihedral_angle_3_deg 12.853 r_dihedral_angle_1_deg 4.922 r_scangle_it 4.466 r_scbond_it 2.754 r_angle_refined_deg 1.595 r_mcangle_it 1.585 r_mcbond_it 0.922 r_chiral_restr 0.127 r_bond_refined_d 0.015 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1831 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 12
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling