3TY1 | pdb_00003ty1

Crystal structure of a putative aldose 1-epimerase (KPN_04629) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.90 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	40.00% 2-methyl-2,4-pentanediol, 0.20M ammonium sulfate, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.033	α = 90
b = 119.953	β = 106.72
c = 103.015	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 325 mm CCD	double crystal monochromator	2011-06-23	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97932,0.97915	SSRL	BL9-2

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	1.9	29.698	99.9	0.074	9.8	3.8	113332	113332			27.331

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	1.9	1.95	100		0.561	0.561	2.3	3.8	8363

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.9	29.698	113323	5671	99.96	0.1598	0.1581	0.1665	0.1931	0.1988	RANDOM	47.1879

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]
0.35		-0.23	-1.32		0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.836
r_dihedral_angle_4_deg	13.788
r_dihedral_angle_3_deg	12.059
r_scangle_it	6.86
r_dihedral_angle_1_deg	5.687
r_scbond_it	4.855
r_mcangle_it	2.8
r_mcbond_it	1.772
r_angle_refined_deg	1.667
r_angle_other_deg	1.232

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.836
r_dihedral_angle_4_deg	13.788
r_dihedral_angle_3_deg	12.059
r_scangle_it	6.86
r_dihedral_angle_1_deg	5.687
r_scbond_it	4.855
r_mcangle_it	2.8
r_mcbond_it	1.772
r_angle_refined_deg	1.667
r_angle_other_deg	1.232
r_mcbond_other	0.544
r_chiral_restr	0.101
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8927
Nucleic Acid Atoms
Solvent Atoms	778
Heterogen Atoms	132

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.