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Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal peptide including Arg17
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 2.8 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.072 α = 90 b = 60.103 β = 124.32 c = 115.703 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 ADSC QUANTUM 210 2004-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 2.1 33.13 94.6 46064 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 2.1 2.17 94.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1WDA 2.1 33.13 2 45630 41436 4628 94.61 0.27 0.20698 0.20251 0.2097 0.24698 0.2497 RANDOM 59.994
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] -5.45 -3.85 4.69 -3.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.363 r_dihedral_angle_3_deg 17.587 r_dihedral_angle_4_deg 15.896 r_dihedral_angle_1_deg 6.833 r_scangle_it 2.289 r_scbond_it 1.49 r_angle_refined_deg 1.467 r_mcangle_it 1.141 r_angle_other_deg 0.969 r_mcbond_it 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.363 r_dihedral_angle_3_deg 17.587 r_dihedral_angle_4_deg 15.896 r_dihedral_angle_1_deg 6.833 r_scangle_it 2.289 r_scbond_it 1.49 r_angle_refined_deg 1.467 r_mcangle_it 1.141 r_angle_other_deg 0.969 r_mcbond_it 0.69 r_symmetry_hbond_refined 0.211 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.205 r_symmetry_vdw_other 0.204 r_xyhbond_nbd_refined 0.194 r_nbd_other 0.184 r_nbtor_refined 0.176 r_mcbond_other 0.124 r_metal_ion_refined 0.117 r_chiral_restr 0.098 r_nbtor_other 0.089 r_xyhbond_nbd_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 4978 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing