6NBG

2.05 Angstrom Resolution Crystal Structure of Hypothetical Protein KP1_5497 from Klebsiella pneumoniae.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP292Protein: 8.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCl pH 8.3; Screen: Classics II (D7), 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG3350;
Crystal Properties
Matthews coefficientSolvent content
2.1843.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.482α = 90
b = 123.806β = 90
c = 299.664γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2018-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-E0.97872APS21-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.053099.80.0950.0950.1050.04420.55.587989-331.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.091000.8320.8320.9220.3930.67625.5

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 DIFFRACTIONSADTHROUGHOUT2.0529.6283398449199.520.202290.200750.23131RANDOM41.545
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]
-1.531.090.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.37
r_dihedral_angle_4_deg12.282
r_dihedral_angle_3_deg8.68
r_long_range_B_refined6.354
r_long_range_B_other6.245
r_dihedral_angle_1_deg2.998
r_scangle_other2.953
r_mcangle_it2.383
r_mcangle_other2.382
r_scbond_it1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.37
r_dihedral_angle_4_deg12.282
r_dihedral_angle_3_deg8.68
r_long_range_B_refined6.354
r_long_range_B_other6.245
r_dihedral_angle_1_deg2.998
r_scangle_other2.953
r_mcangle_it2.383
r_mcangle_other2.382
r_scbond_it1.98
r_scbond_other1.92
r_mcbond_it1.54
r_mcbond_other1.54
r_angle_refined_deg1.469
r_angle_other_deg0.377
r_chiral_restr0.067
r_gen_planes_refined0.054
r_gen_planes_other0.052
r_bond_refined_d0.006
r_bond_other_d0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11006
Nucleic Acid Atoms
Solvent Atoms763
Heterogen Atoms41

Software

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