2NVA | pdb_00002nva

The X-ray crystal structure of the Paramecium bursaria Chlorella virus arginine decarboxylase bound to agmatine

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NV9	PDB ENTRY 2NV9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	6% PEG-8000, 100 mM imidazole, 200 mM calcium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.206	α = 90
b = 117.275	β = 90
c = 268.65	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 315	Mirrors	2005-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97945	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.8	50	99.8	0.111	14.7		337817	337027	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	100		0.249			33474

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2NV9	1.8	44.74	337027	336913	2052	99.73	0.2187	0.219	0.219	0.2327	0.238	0.2573	RANDOM	14.139

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]
0.32			0.37		-0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.576
r_dihedral_angle_4_deg	15.734
r_dihedral_angle_3_deg	12.381
r_dihedral_angle_1_deg	5.999
r_scangle_it	1.425
r_angle_refined_deg	1.186
r_scbond_it	1.065
r_mcangle_it	0.574
r_mcbond_it	0.483
r_nbtor_refined	0.311
r_nbd_refined	0.192
r_symmetry_vdw_refined	0.191
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.114
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23375
Nucleic Acid Atoms
Solvent Atoms	1467
Heterogen Atoms	192

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
CNS	phasing