2DEW

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal tail including Arg8


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
2.956.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.268α = 90
b = 60.773β = 124.26
c = 115.146γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.000SPring-8BL38B1

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
12.138.3497.94800322
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1797.9

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 REPLACEMENTTHROUGHOUT1WDA2.138.3424312643126487897.880.2720.205750.201860.24078RANDOM47.473
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]
-3.97-2.913.63-2.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.41
r_dihedral_angle_3_deg18.467
r_dihedral_angle_4_deg16.37
r_dihedral_angle_1_deg6.844
r_scangle_it2.282
r_scbond_it1.511
r_angle_refined_deg1.465
r_mcangle_it1.108
r_angle_other_deg0.849
r_mcbond_it0.682
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.41
r_dihedral_angle_3_deg18.467
r_dihedral_angle_4_deg16.37
r_dihedral_angle_1_deg6.844
r_scangle_it2.282
r_scbond_it1.511
r_angle_refined_deg1.465
r_mcangle_it1.108
r_angle_other_deg0.849
r_mcbond_it0.682
r_symmetry_hbond_refined0.29
r_nbd_refined0.21
r_symmetry_vdw_refined0.191
r_nbd_other0.186
r_xyhbond_nbd_refined0.179
r_nbtor_refined0.177
r_symmetry_vdw_other0.154
r_mcbond_other0.133
r_metal_ion_refined0.124
r_chiral_restr0.092
r_nbtor_other0.087
r_bond_refined_d0.012
r_bond_other_d0.004
r_gen_planes_refined0.004
r_gen_planes_other0.001
r_xyhbond_nbd_other
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 Atoms4990
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms20

Software

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