2BKX

Structure and kinetics of a monomeric glucosamine-6-phosphate deaminase: missing link of the NagB superfamily


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BKVPDB ENTRY 2BKV

Crystallization

Crystal Properties
Matthews coefficientSolvent content
1.6625.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.966α = 90
b = 47.898β = 90.06
c = 71.397γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.43092.90.0615.833.6781482
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)
11.41.4561.60.314.313.2

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 2BKV1.470.7178127389892.70.1220.1190.165RANDOM9.8
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]
0.059-0.071-0.1620.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.514
r_dihedral_angle_4_deg14.947
r_dihedral_angle_3_deg13.532
r_dihedral_angle_1_deg5.76
r_scangle_it5.122
r_scbond_it3.866
r_mcangle_it2.194
r_mcbond_it1.985
r_angle_other_deg1.972
r_angle_refined_deg1.658
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.514
r_dihedral_angle_4_deg14.947
r_dihedral_angle_3_deg13.532
r_dihedral_angle_1_deg5.76
r_scangle_it5.122
r_scbond_it3.866
r_mcangle_it2.194
r_mcbond_it1.985
r_angle_other_deg1.972
r_angle_refined_deg1.658
r_nbd_refined0.238
r_symmetry_vdw_refined0.223
r_symmetry_vdw_other0.206
r_nbd_other0.203
r_symmetry_hbond_refined0.2
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.176
r_chiral_restr0.116
r_nbtor_other0.098
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms3796
Nucleic Acid Atoms
Solvent Atoms730
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing