1RKQ

Crystal structure of HAD-like phosphatase yidA from E. coli

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Experimental Phasing by single crystal SIRAS (Radiation damage).

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	PEG 3350, Magnesium Chloride,, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.12	α = 112.58
b = 54.871	β = 96.37
c = 67.725	γ = 106.79

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	MARRESEARCH		2003-08-06	M	SINGLE WAVELENGTH
2	1	x-ray	120	CCD	MARRESEARCH		2003-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9A	0.97901	NSLS	X9A
2	SYNCHROTRON	NSLS BEAMLINE X9A	1.0083	NSLS	X9A

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
1,2	1.4	24	95.9	0.043	0.064	30.9	3.7	106331	106331			16.8

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)
	1.4	1.45	93.4		0.37	0.56	2.58		10374

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	Single Crystal SIRAS by RIP	Throught	Experimental Phasing by single crystal SIRAS (Radiation damage).	1.4	24.5	99828	99828	5253	95.5	0.185	0.177	0.213	RANDOM

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	22.2
p_staggered_tor	13.4
p_planar_tor	6.2
p_multtor_nbd	0.269
p_singtor_nbd	0.168
p_chiral_restr	0.139
p_xyhbond_nbd	0.105
p_planar_d	0.04
p_angle_d	0.034
p_plane_restr	0.031
p_bond_d	0.02
p_angle_deg
p_hb_or_metal_coord
p_mcbond_it
p_mcangle_it
p_scbond_it
p_scangle_it
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4208
Nucleic Acid Atoms
Solvent Atoms	612
Heterogen Atoms	10

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXE	model building
RESOLVE	model building
ARP/wARP	model building
REFMAC	refinement
RESOLVE	phasing