2BI7

udp-galactopyranose mutase from Klebsiella pneumoniae oxidised 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 = 85.675α = 90
b = 85.675β = 90
c = 99.793γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IVMIRRORS2003-07-15MSINGLE 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
1274.5498.10.0510.616.62160
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)
122.1288.60.174.39.1

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 1I8T274.54243521293880.1950.1930.247RANDOM34.83
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]
0.180.090.18-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.531
r_dihedral_angle_4_deg18.947
r_dihedral_angle_3_deg15.493
r_dihedral_angle_1_deg5.567
r_scangle_it2.39
r_scbond_it1.623
r_angle_refined_deg1.203
r_mcangle_it1.023
r_mcbond_it0.613
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.531
r_dihedral_angle_4_deg18.947
r_dihedral_angle_3_deg15.493
r_dihedral_angle_1_deg5.567
r_scangle_it2.39
r_scbond_it1.623
r_angle_refined_deg1.203
r_mcangle_it1.023
r_mcbond_it0.613
r_nbtor_refined0.308
r_symmetry_hbond_refined0.261
r_nbd_refined0.206
r_xyhbond_nbd_refined0.158
r_symmetry_vdw_refined0.145
r_chiral_restr0.081
r_bond_refined_d0.01
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 Atoms140
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing