3ITK

Crystal structure of human UDP-glucose dehydrogenase Thr131Ala, apo form.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q3EPDB ENTRY 2Q3E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16293.1515% PEG smears (PEG 400, 600, 1000, 2000, 3350, 4000, MME 5000, 6000, 8000, 10000), 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.6553.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.06α = 90
b = 106.61β = 90
c = 349.12γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2009-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.452.999.80.1317.94130411240.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5399.40.552.13.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2Q3E2.452.9130411128277213499.70.1990.1980.241RANDOM12.77
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]
-0.230.37-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.487
r_dihedral_angle_4_deg17.501
r_dihedral_angle_3_deg13.546
r_scangle_it7.877
r_scbond_it5.506
r_dihedral_angle_1_deg5.449
r_mcangle_it3.257
r_mcbond_it1.793
r_angle_refined_deg1.463
r_angle_other_deg1.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.487
r_dihedral_angle_4_deg17.501
r_dihedral_angle_3_deg13.546
r_scangle_it7.877
r_scbond_it5.506
r_dihedral_angle_1_deg5.449
r_mcangle_it3.257
r_mcbond_it1.793
r_angle_refined_deg1.463
r_angle_other_deg1.096
r_mcbond_other0.618
r_chiral_restr0.083
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.003
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21621
Nucleic Acid Atoms
Solvent Atoms1188
Heterogen Atoms133

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling