3KYB

Structure of UDP-galactopyranose mutase bound to flavin mononucleotide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GF4PDB ENTRY 3GF4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6298DROPS CONTAINING 1.5 MICROLITERS 5 MG/ML PROTEIN IN 20 MM HEPES PH 7.0 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. CRYSTAL WAS THEN SOAKED IN A SOLUTION OF 53% QIAGEN CRYOS SUITE CONDITION #87 WITH 15 MM L-CYS AND 23 MM FLAVIN MONONUCLEOTIDE (24HRS). CRYSTAL WAS BRIEFLY SOAKED (20 SECONDS) IN A SOLUTION OF 53% QIAGEN CRYOS SUITE CONDITION #87 WITH 15 MM L-CYS, 30% METHANOL, 10 MM FLAVIN MONONUCLEOTIDE PRIOR TO VITRIFICATION, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.1360.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.8α = 90
b = 93.8β = 90
c = 128.8γ = 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-G0.97857APS21-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
12.3501000.093177.6494964947239.2
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)
2.32.381000.2867.27.34912

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3GF42.3304687946820249999.870.1850.1850.1830.221RANDOM32.6
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]
-0.71-0.711.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.137
r_dihedral_angle_4_deg16.9
r_dihedral_angle_3_deg16.464
r_dihedral_angle_1_deg6.697
r_scangle_it5.403
r_scbond_it3.469
r_mcangle_it2.215
r_angle_refined_deg2.007
r_mcbond_it1.229
r_chiral_restr0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.137
r_dihedral_angle_4_deg16.9
r_dihedral_angle_3_deg16.464
r_dihedral_angle_1_deg6.697
r_scangle_it5.403
r_scbond_it3.469
r_mcangle_it2.215
r_angle_refined_deg2.007
r_mcbond_it1.229
r_chiral_restr0.14
r_bond_refined_d0.025
r_gen_planes_refined0.011
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 Atoms6227
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms230

Software

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