3P7I | pdb_00003p7i

Crystal structure of Escherichia coli PhnD in complex with 2-aminoethyl phosphonate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298.15	0.2M ammonium sulfate, sodium acetate trihydrate, pH 4.6, 25% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.094	α = 90
b = 82.44	β = 90
c = 54.667	γ = 90

Symmetry
Space Group	P 21 21 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	MAR CCD 165 mm		2009-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

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	1.71	45.6	99.6			35864	35721

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.71	45.6	35864	35721	1880	99.6	0.22697	0.22697	0.22568	0.2185	0.25144	0.2474	RANDOM	25.239

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]
			-0.04		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.228
r_dihedral_angle_4_deg	18.994
r_dihedral_angle_3_deg	16.728
r_dihedral_angle_1_deg	5.956
r_scangle_it	5.051
r_scbond_it	3.215
r_mcangle_it	2.077
r_angle_refined_deg	2.021
r_mcbond_it	1.319
r_chiral_restr	0.151
r_bond_refined_d	0.026
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2353
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms	25

Software

Software
Software Name	Purpose
SPEC	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling