2BI8

udp-galactopyranose mutase from Klebsiella pneumoniae with reduced FAD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I8TPDB ENTRY 1I8T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1M BIS-TRIS PH6.5,50MM CACL2, 30% PEG550, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.3547

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.997α = 90
b = 85.997β = 90
c = 100.809γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IVMIRRORS2004-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
12.3527.1299.50.069.52.518331
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)
12.352.4899.10.481.62.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1I8T2.3527.121740591499.50.190.1870.243RANDOM62.7
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]
-1.02-0.51-1.021.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.375
r_dihedral_angle_3_deg17.836
r_dihedral_angle_4_deg14.985
r_dihedral_angle_1_deg6.201
r_scangle_it1.992
r_scbond_it1.295
r_angle_refined_deg1.23
r_mcangle_it0.857
r_mcbond_it0.481
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.375
r_dihedral_angle_3_deg17.836
r_dihedral_angle_4_deg14.985
r_dihedral_angle_1_deg6.201
r_scangle_it1.992
r_scbond_it1.295
r_angle_refined_deg1.23
r_mcangle_it0.857
r_mcbond_it0.481
r_nbtor_refined0.309
r_symmetry_hbond_refined0.247
r_nbd_refined0.221
r_xyhbond_nbd_refined0.17
r_symmetry_vdw_refined0.132
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3118
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing