4PGL | pdb_00004pgl

Crystal structure of engineered D-tagatose 3-epimerase PcDTE-ILS6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QUL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.7	293	0.1M MES, 10% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.81	α = 90
b = 47.44	β = 102.49
c = 126.38	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	PIXEL	DECTRIS PILATUS 2M-F		2013-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0000	SLS	X06DA

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	2.1	36.85	99.1	0.107	12.1	6.2		69460

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	2.1	2.15	98.4		0.471	3.7	5.8

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2QUL	2.1	36.85	69447	3506	98.7	0.152	0.1626	0.181	0.1869	RANDOM	15.65

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]
-0.59		-1.52	-0.29		1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.411
r_dihedral_angle_4_deg	17.16
r_dihedral_angle_3_deg	13.932
r_dihedral_angle_1_deg	6.345
r_angle_refined_deg	1.398
r_angle_other_deg	1.041
r_chiral_restr	0.083
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_gen_planes_other	0.008
r_bond_other_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9334
Nucleic Acid Atoms
Solvent Atoms	367
Heterogen Atoms	161

Software

Software
Software Name	Purpose
Coot	model building
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing