2A3L | pdb_00002a3l

X-Ray Structure of Adenosine 5'-Monophosphate Deaminase from Arabidopsis Thaliana in Complex with Coformycin 5'-Phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		RABBIT AMPD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6	295	8 MG/ML PROTEIN, 0.40 M MONOAMMONIUM DIHYDROGEN PHOSPHATE, 0.10 M TRI-SODIUM CITRATE, 10% (V/V) ETHANOL, vapor diffusion, hanging drop, temperature 295K, pH 5.60

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.325	α = 90
b = 131.325	β = 90
c = 208.254	γ = 120

Symmetry
Space Group	P 62 2 2

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 300 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-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	3.34	50	99.6	0.06	22.579	6.1		16001

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	3.34	3.42	99.5		0.489	3.922	5.7

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	RABBIT AMPD	3.34	49.91	15038	741	93.8	0.237	0.237	0.22	0.323	0.31	RANDOM	73.5

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]
10.914	-1.407		10.914		-21.828

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.8
c_angle_deg	2.4
c_improper_angle_d	1.48
c_bond_d	0.016
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5050
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	30

Software

Software
Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction