3KHU | pdb_00003khu

Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q3E	PDB entry 2Q3E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277.15	18% PEG smears (PEG 400, 600, 1000, 2000, 3350, 4000, 5000 MME, 6000, 8000, 10000), 0.1M HEPES pH 7.5, 5% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 203.54	α = 90
b = 207.34	β = 90
c = 93.4	γ = 90

Symmetry
Space Group	P 21 21 2

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	ADSC QUANTUM 315	mirrors	2009-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	2.3	48.74	99.8	0.106	9.4	4.3	175207	175139		2

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	2.3	2.42	100		0.743	2	4.3	25412

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2Q3E	2.3	48.74	175128	173128	1988	99.71	0.19544	0.19509	0.2	0.2252	0.23	RANDOM	19.743

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]
-3.2			0.75		2.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.178
r_dihedral_angle_4_deg	20.67
r_dihedral_angle_3_deg	13.744
r_scangle_it	7.651
r_scbond_it	5.293
r_dihedral_angle_1_deg	5.28
r_mcangle_it	2.975
r_mcbond_it	1.593
r_angle_refined_deg	1.438
r_angle_other_deg	1.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.178
r_dihedral_angle_4_deg	20.67
r_dihedral_angle_3_deg	13.744
r_scangle_it	7.651
r_scbond_it	5.293
r_dihedral_angle_1_deg	5.28
r_mcangle_it	2.975
r_mcbond_it	1.593
r_angle_refined_deg	1.438
r_angle_other_deg	1.007
r_mcbond_other	0.326
r_chiral_restr	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21667
Nucleic Acid Atoms
Solvent Atoms	1314
Heterogen Atoms	515

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.