5UEJ

1.30 A crystal structure of DapE enzyme from Neisseria meningitidis MC58


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.2 M Lithium Sulfate, 0.1 M Tris:HCl pH 8.5, 1.26 M Ammonium Sulfate, 0.05 M DMSO
Crystal Properties
Matthews coefficientSolvent content
2.6854.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.767α = 90
b = 88.644β = 90
c = 133.402γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6MDouble Crystal2016-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9795APS19-ID

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
11.34099.40.08227.4217263
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.32

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.340176526943995.20.114970.1130.15254RANDOM18.628
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]
0.12-0.170.05
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.399
r_dihedral_angle_2_deg35.703
r_dihedral_angle_4_deg17.956
r_sphericity_bonded16.081
r_dihedral_angle_3_deg12.639
r_scangle_other6.626
r_long_range_B_refined6.391
r_dihedral_angle_1_deg6.122
r_scbond_other6.071
r_scbond_it6.068
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.399
r_dihedral_angle_2_deg35.703
r_dihedral_angle_4_deg17.956
r_sphericity_bonded16.081
r_dihedral_angle_3_deg12.639
r_scangle_other6.626
r_long_range_B_refined6.391
r_dihedral_angle_1_deg6.122
r_scbond_other6.071
r_scbond_it6.068
r_rigid_bond_restr5.749
r_long_range_B_other5.566
r_mcbond_other2.867
r_mcbond_it2.866
r_mcangle_it2.863
r_mcangle_other2.863
r_angle_refined_deg2.435
r_angle_other_deg1.322
r_chiral_restr0.179
r_bond_refined_d0.029
r_gen_planes_refined0.014
r_gen_planes_other0.004
r_bond_other_d0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5736
Nucleic Acid Atoms
Solvent Atoms1129
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing