2DEX

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

X-RAY DIFFRACTION

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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	R-Free	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	0.24698	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
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