3GMZ | pdb_00003gmz

Crystal of human arginase in complex with L-ornithine. Resolution 1.43 A.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZAV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	298	Crystalline DFMO and L-ornithine complexes with human arginase I were prepared by soaking these ligands into pre-formed crystals of the native enzyme, which were prepared by the hanging drop vapor diffusion method at 21 C. Typically, drops containing 3 uL of protein solution [3.5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM thymine, 100 uM MnCl2] and 3 uL of precipitant solution [0.1 M bis-Tris (pH 6.5), 28% PEG monomethyl ether 2000] were equilibrated over a 1 mL reservoir of precipitant solution. VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.392	α = 90
b = 90.392	β = 90
c = 69.422	γ = 120

Symmetry
Space Group	P 3

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 315		2008-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.0	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.43	50	99.8	0.067	0.067	35.6		116771	116771

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.43	1.53	100		0.64	0.64	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	2ZAV	1.43	50	111891	111891	5513		0.147	0.1499	0.185	0.1509	throughout	20.503

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]
-1.068	-0.75		-1.068		2.137

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.206
c_scbond_it	1.572
c_mcangle_it	1.503
c_mcbond_it	0.966

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4790
Nucleic Acid Atoms
Solvent Atoms	393
Heterogen Atoms	22

Software

Software
Software Name	Purpose
ADSC	data collection
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing