5ME4

The structure of HtxB from Pseudomonas stutzeri in complex with hypophosphite to 1.52 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JVB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52830.2 M Sodium/potassium tartrate, 0.1 M Bis-tris propane pH 8.5 and 20 % (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2946.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.24α = 90
b = 55.21β = 90
c = 125.2γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.97951DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.5222.8197.70.1170.9989.87.142787
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.521.5591.31.2090.5251.16

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 REPLACEMENTTHROUGHOUT5JVB1.5222.840628211597.520.16880.167320.19771RANDOM23.139
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]
1.11-0.3-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.995
r_scbond_it20.396
r_scbond_other20.39
r_dihedral_angle_4_deg19.739
r_scangle_other15.464
r_long_range_B_other15.108
r_long_range_B_refined15.035
r_dihedral_angle_3_deg13.171
r_dihedral_angle_1_deg5.891
r_mcangle_it4.725
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.995
r_scbond_it20.396
r_scbond_other20.39
r_dihedral_angle_4_deg19.739
r_scangle_other15.464
r_long_range_B_other15.108
r_long_range_B_refined15.035
r_dihedral_angle_3_deg13.171
r_dihedral_angle_1_deg5.891
r_mcangle_it4.725
r_mcangle_other4.724
r_mcbond_it4.277
r_mcbond_other4.075
r_angle_refined_deg1.453
r_angle_other_deg0.923
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms2000
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing