1XM5 | pdb_00001xm5

Crystal structure of metal-dependent hydrolase ybeY from E. coli, Pfam UPF0054

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	278	PEG3350, magnesium chloride, Bis Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.61	51.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.073	α = 90
b = 119.613	β = 90
c = 132.903	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	MARRESEARCH		2004-06-28	M	SINGLE WAVELENGTH
2	1	x-ray	110	CCD	MARRESEARCH		2004-06-28	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.97919	NSLS	X29A
2	SYNCHROTRON	NSLS BEAMLINE X29A	0.97938, 0.97919, 0.96408	NSLS	X29A

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
1,2	2.7	25	97.9			20911	20911

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.8	99.5

Refinement

Statistics
Diffraction ID	Structure Solution 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	MAD	2.7	25	18232	18232	894		0.239	0.239	0.234	0.2415	0.273	0.2797	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
c_angle_deg	1.2
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4777
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	4

Software

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