3INR | pdb_00003inr

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GF4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6298Drops 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 coefficientSolvent content
3.1360.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.799α = 90
b = 93.799β = 90
c = 128.584γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDberyllium lens2008-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.33098.50.08515.45.94942448652
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.32.3898.40.2667.15.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3GF42.3304684646068242198.340.189670.187410.180.233050.22RANDOM33.693
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]
-1.07-1.072.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.888
r_dihedral_angle_4_deg18.787
r_dihedral_angle_3_deg15.807
r_dihedral_angle_1_deg6.467
r_scangle_it4.745
r_scbond_it3.122
r_mcangle_it2.005
r_angle_refined_deg1.811
r_mcbond_it1.103
r_chiral_restr0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.888
r_dihedral_angle_4_deg18.787
r_dihedral_angle_3_deg15.807
r_dihedral_angle_1_deg6.467
r_scangle_it4.745
r_scbond_it3.122
r_mcangle_it2.005
r_angle_refined_deg1.811
r_mcbond_it1.103
r_chiral_restr0.127
r_bond_refined_d0.022
r_gen_planes_refined0.01
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 AtomsNumber
Protein Atoms6203
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms178

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling