Experiment: 4YTR

Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with 1-deoxy L-tagatose

X-RAY DIFFRACTION

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, HANGING DROP	4.6	293	6-9 % PEG4000, 0.1 M Sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.38	α = 90
b = 126.33	β = 98.7
c = 92.92	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	IMAGE PLATE	RIGAKU RAXIS VII		2012-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.9	22.14	98.2	0.085	8.7	2.92		92108			15.9

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	1.9	1.97	85.2		0.299	3.4	2.45	7957

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-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	2QUL	1.9	21.71	92074	9204	98	0.193	0.188	0.1834	0.235	0.23	RANDOM	21

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]
-1.94		-1.37	-0.65		2.59

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.4
c_scangle_it	2.73
c_scbond_it	1.96
c_mcangle_it	1.79
c_mcbond_it	1.21
c_angle_deg	1.2
c_improper_angle_d	0.77
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9283
Nucleic Acid Atoms
Solvent Atoms	1151
Heterogen Atoms	114

Software

Software
Software Name	Purpose
CNS	refinement
d*TREK	data reduction
PDB_EXTRACT	data extraction
CrystalClear	data scaling
MOLREP	phasing