2DEY | pdb_00002dey

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H4 N-terminal tail including Arg3

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
2.9	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-Work (DCC)	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	0.21	0.24846	0.25	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
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