☰ Navigation Tabs
Crystal structure of human peptidylarginine deiminase 4 in complex with histone H4 N-terminal tail including Arg3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1M Imidazole (pH8.0), 0.2M lithium sulfate, 10% PEGMME2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.9 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.192 α = 90 b = 60.611 β = 124.18 c = 115.203 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 273 CCD ADSC QUANTUM 4 2004-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 SPring-8 BL38B1
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 2.25 33.57 98.3 39243 2 2
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 2.25 2.33 98.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1WDA 2.25 33.57 2 39238 35325 3918 98.3 0.275 0.20443 0.19946 0.24846 0.2949 RANDOM 55.294
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] -4.67 -3.39 4.3 -3.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.356 r_dihedral_angle_4_deg 20.837 r_dihedral_angle_3_deg 19.015 r_dihedral_angle_1_deg 7.397 r_scangle_it 2.444 r_angle_refined_deg 1.622 r_scbond_it 1.599 r_mcangle_it 1.228 r_angle_other_deg 0.872 r_mcbond_it 0.748
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.356 r_dihedral_angle_4_deg 20.837 r_dihedral_angle_3_deg 19.015 r_dihedral_angle_1_deg 7.397 r_scangle_it 2.444 r_angle_refined_deg 1.622 r_scbond_it 1.599 r_mcangle_it 1.228 r_angle_other_deg 0.872 r_mcbond_it 0.748 r_symmetry_hbond_refined 0.448 r_nbd_refined 0.21 r_nbd_other 0.189 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_other 0.145 r_mcbond_other 0.134 r_symmetry_vdw_refined 0.121 r_metal_ion_refined 0.112 r_chiral_restr 0.095 r_nbtor_other 0.09 r_xyhbond_nbd_other 0.065 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4980 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing