3B1T | pdb_00003b1t

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

X-RAY DIFFRACTION

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	0.26	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

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.