2JKB

Crystal structure of Streptococcus pneumoniae NanB in complex with 2, 7-anhydro-Neu5Ac


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelOtherHOMOLOGY MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
112% PEG 6000, 200 MM TRIS PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.4449.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.719α = 90
b = 82.746β = 90
c = 118.079γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONICSTOROIDAL MIRRORMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.542597.10.0619.33.6108114-3
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)
11.541.681.60.352.63

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 REPLACEMENTTHROUGHOUTHOMOLOGY MODEL1.5423.93105364267797.10.1630.1620.188RANDOM12.31
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]
-0.020.03-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.57
r_dihedral_angle_4_deg13.412
r_dihedral_angle_3_deg11.123
r_dihedral_angle_1_deg6.919
r_scangle_it2.555
r_scbond_it1.912
r_angle_refined_deg1.344
r_mcangle_it1.102
r_mcbond_it0.984
r_angle_other_deg0.803
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.57
r_dihedral_angle_4_deg13.412
r_dihedral_angle_3_deg11.123
r_dihedral_angle_1_deg6.919
r_scangle_it2.555
r_scbond_it1.912
r_angle_refined_deg1.344
r_mcangle_it1.102
r_mcbond_it0.984
r_angle_other_deg0.803
r_symmetry_vdw_other0.315
r_symmetry_vdw_refined0.226
r_nbd_other0.194
r_nbd_refined0.19
r_nbtor_refined0.176
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.137
r_nbtor_other0.082
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms5213
Nucleic Acid Atoms
Solvent Atoms1024
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing