3INR

Structure of UDP-galactopyranose mutase bound to UDP-galactose (oxidized)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GF4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	Drops containing 1.5 microliters 5 mg/mL protein in 20 mM HEPES were combined with 1.5 microliters well solution (85 mM ammonium acetate, 42 mM tri-sodium citrate, 12.3% PEG 4000, 7.5% glycerol, 15 mM L-cysteine, 5 mM UDP-Glc) for 1-2 weeks. Crystals were then soaked in a solution of 53% Qiagen Cryos Suite Condition #87 with 15 mM L-cys, 30% methanol, 90 mM UDP-Galp (24hrs), pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.799	α = 90
b = 93.799	β = 90
c = 128.584	γ = 90

Symmetry
Space Group	P 41

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 300 mm CCD	beryllium lens	2008-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.3	30	98.5	0.085	15.4	5.9	49424	48652

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)
	2.3	2.38	98.4		0.266	7.1	5.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3GF4	2.3	30	46846	46068	2421	98.34	0.18967	0.18741	0.23305	RANDOM	33.693

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]
-1.07			-1.07		2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.888
r_dihedral_angle_4_deg	18.787
r_dihedral_angle_3_deg	15.807
r_dihedral_angle_1_deg	6.467
r_scangle_it	4.745
r_scbond_it	3.122
r_mcangle_it	2.005
r_angle_refined_deg	1.811
r_mcbond_it	1.103
r_chiral_restr	0.127
r_bond_refined_d	0.022
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6203
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	178

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling