3HDY | pdb_00003hdy

Crystal Structure of UDP-galactopyranose mutase (reduced form) in complex with substrate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1V0J	PDB entry 1V0J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.5	295	0.1 M HEPES pH 6.5, 0.2 M LiCl and 28 % PEG 6000, Microbatch, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.82	α = 90
b = 174.628	β = 90
c = 218.192	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		CCD	MARMOSAIC 225 mm CCD		2009-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9797	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	39.94	95.8	0.187	0.187	5.1	4.7		189435	0.5	0.5

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)
	2.4	2.49	92.1		0.635	1.7	4.34	78255

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB entry 1V0J	2.4	39.94	1.34	189334	9505	95.76	0.2377	0.2355	0.24	0.2801	0.28

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	19.081
f_angle_d	0.749
f_chiral_restr	0.049
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	29444
Nucleic Acid Atoms
Solvent Atoms	556
Heterogen Atoms	890

Software

Software
Software Name	Purpose
PHENIX	refinement

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.