3B1U

Crystal structure of human peptidylarginine deiminase 4 in complex with o-F-amidine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.422	α = 90
b = 60.468	β = 124.43
c = 115.506	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 270		2009-12-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1	Photon Factory	BL-17A

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	50					44771

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1WDA	2.1	20	42464	2254	100	0.22086	0.21928	0.2502	RANDOM	79.135

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]
-3.52		-2.67	2.83		-2.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.774
r_dihedral_angle_3_deg	13.767
r_dihedral_angle_4_deg	13.693
r_dihedral_angle_1_deg	5.551
r_angle_other_deg	3.025
r_angle_refined_deg	0.887
r_scangle_it	0.794
r_mcangle_it	0.485
r_scbond_it	0.467
r_mcbond_it	0.261
r_chiral_restr	0.055
r_mcbond_other	0.028
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_gen_planes_other	0.002
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	4947
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement