2DEX

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal peptide including Arg17


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WDA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82930.1M Imidazole (pH8.0), 0.2M lithium sulfate, 10% PEGMME2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.856.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.072α = 90
b = 60.103β = 124.32
c = 115.703γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.133.1394.64606422
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1794.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1WDA2.133.1324563041436462894.610.270.206980.202510.24698RANDOM59.994
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]
-5.45-3.854.69-3.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.363
r_dihedral_angle_3_deg17.587
r_dihedral_angle_4_deg15.896
r_dihedral_angle_1_deg6.833
r_scangle_it2.289
r_scbond_it1.49
r_angle_refined_deg1.467
r_mcangle_it1.141
r_angle_other_deg0.969
r_mcbond_it0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.363
r_dihedral_angle_3_deg17.587
r_dihedral_angle_4_deg15.896
r_dihedral_angle_1_deg6.833
r_scangle_it2.289
r_scbond_it1.49
r_angle_refined_deg1.467
r_mcangle_it1.141
r_angle_other_deg0.969
r_mcbond_it0.69
r_symmetry_hbond_refined0.211
r_nbd_refined0.21
r_symmetry_vdw_refined0.205
r_symmetry_vdw_other0.204
r_xyhbond_nbd_refined0.194
r_nbd_other0.184
r_nbtor_refined0.176
r_mcbond_other0.124
r_metal_ion_refined0.117
r_chiral_restr0.098
r_nbtor_other0.089
r_xyhbond_nbd_other0.083
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms4978
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing