6HZI | pdb_00006hzi

Apo structure of TP domain from Burkholderia pseudomallei penicillin-binding protein 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5UY7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27725% (w/v) polyethylene glycol 3,350 and 0.3 M sodium formate
Crystal Properties
Matthews coefficientSolvent content
3.4163.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.394α = 90
b = 106.394β = 90
c = 95.678γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.98DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
12.2953.21000.3119.425.625371
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.292.33

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5uy72.2953.22531099.940.196060.196060.245.754
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]
-1.3-1.32.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.667
r_dihedral_angle_4_deg20.022
r_dihedral_angle_3_deg12.838
r_long_range_B_other11.867
r_long_range_B_refined11.847
r_scangle_other8.303
r_dihedral_angle_1_deg6.925
r_mcangle_other6.895
r_mcangle_it6.884
r_scbond_it5.671
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2486
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MrBUMPphasing