2Q3E | pdb_00002q3e

Structure of human UDP-glucose dehydrogenase complexed with NADH and UDP-glucose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O3J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	16% PEG 3350, 8% EG, 160 mM NaBr, 80 mM BTP., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.99	α = 90
b = 184.132	β = 109.23
c = 170.943	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	CCD	MARMOSAIC 225 mm CCD		2007-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9999	SLS	X10SA

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	50	99.6	0.089	9.7	3.9	452865	452865			28

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	2.11	99.1		0.636	2	3.9	65636

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 (All)	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	2o3j	2	49.09	429343	429343	23473	100	0.17343	0.17343	0.17163	0.1763	0.20521	0.2092	THIN SHELLS	26.333

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]
1.82		2.37	-1.26		1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.976
r_dihedral_angle_4_deg	17.948
r_dihedral_angle_3_deg	12.539
r_scangle_it	5.266
r_dihedral_angle_1_deg	5.244
r_scbond_it	3.894
r_mcangle_it	2.275
r_mcbond_it	1.647
r_angle_refined_deg	1.234
r_angle_other_deg	0.943
r_mcbond_other	0.57
r_symmetry_vdw_other	0.266
r_nbd_refined	0.194
r_nbd_other	0.185
r_symmetry_hbond_refined	0.181
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.128
r_symmetry_vdw_refined	0.09
r_nbtor_other	0.082
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	42755
Nucleic Acid Atoms
Solvent Atoms	2745
Heterogen Atoms	972

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing