5LU0

Crystal structure of H. pylori referent strain in complex with PO4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherPNP from E. Coli

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72910.1 M Tris, 10 % PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.2344.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.52α = 90
b = 86.31β = 90
c = 268.449γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R0.97957ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.73134.228728.8811133010
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.79923.8611.9

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 REPLACEMENTTHROUGHOUTPNP from E. Coli1.73134.22126978622887.290.18590.18380.2277RANDOM17.1663
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.636
r_dihedral_angle_4_deg18.791
r_dihedral_angle_3_deg16.428
r_dihedral_angle_1_deg6.722
r_mcangle_it1.842
r_angle_refined_deg1.726
r_scbond_it1.685
r_mcbond_it1.156
r_chiral_restr0.167
r_bond_refined_d0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.636
r_dihedral_angle_4_deg18.791
r_dihedral_angle_3_deg16.428
r_dihedral_angle_1_deg6.722
r_mcangle_it1.842
r_angle_refined_deg1.726
r_scbond_it1.685
r_mcbond_it1.156
r_chiral_restr0.167
r_bond_refined_d0.014
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10812
Nucleic Acid Atoms
Solvent Atoms1354
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
iMOSFLMdata reduction
PHENIXphasing