4E4J | pdb_00004e4j

Crystal structure of arginine deiminase from Mycoplasma penetrans

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7		1.7 M Ammonium sulfate, pH 7 bis-tris 0.1M amb 15% glyOH, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.548	α = 90
b = 128.875	β = 91.41
c = 220.279	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD	(111) monochromator and Pt coated mirrors in a Kirkpatrick-Baez configuration	2011-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	2.3	30	97.6	0.06	9.8	1.9	290893	290893

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2.3	30	1971	288889	14608	96.9	0.2097	0.21	0.2385	0.24	34.7898

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]
0.937		-1.039	-5.811		4.874

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.931
c_mcangle_it	2.087
c_scbond_it	1.977
c_angle_d	1.325
c_mcbond_it	1.271
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	38004
Nucleic Acid Atoms
Solvent Atoms	1615
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction

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.