3B1T | pdb_00003b1t

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WDA	PDB ENTRY 1WDA

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
2.8	56.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.787	α = 90
b = 60.853	β = 123.99
c = 114.302	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	2.5	50					27393

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1WDA	2.5	20	27346	1367	100	0.2138	0.2111	0.21	0.2629	0.2562	RANDOM	75.845

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]
-2.54		-1.86	2.18		-1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.697
r_dihedral_angle_3_deg	20.079
r_dihedral_angle_4_deg	18.219
r_dihedral_angle_1_deg	7.455
r_angle_other_deg	3.379
r_angle_refined_deg	1.484
r_chiral_restr	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4912
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement