Experiment: 4HGR

Crystal structure of E56A/K67A mutant of 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase from Bacteroides thetaiotaomicron

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3E8M	PDB entry 3E8M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	100 mM Hepes, 150 mM magnesium chloride, 25% polyethylene glycol 3350, 3% dioxane. The crystal was dragged through paratone prior to flash-cooling, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.367	α = 90
b = 116.765	β = 93.09
c = 75.18	γ = 90

Symmetry
Space Group	P 1 21 1

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	Bruker Platinum 135	Helios multi-layer optics	2010-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.05	50.73	97.4	0.1308	14.12	10.66	76062	76062	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.15	92.7		0.4769	3.73	6.78	9626

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB entry 3E8M	2.05	50.715	1.34	76062	76062	3977	97.36	0.1926	0.1899	0.1959	0.2412	0.2475	Random	20.48

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
f_dihedral_angle_d	14.602
f_angle_d	0.922
f_chiral_restr	0.065
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10198
Nucleic Acid Atoms
Solvent Atoms	700
Heterogen Atoms	8

Software

Software
Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
PHENIX	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling