7QZR

Structure of native leukocyte myeloperoxidase in complex with the Staphyloccal Peroxidase Inhibitor SPIN from Staphylococcus aureus


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92988% (w/V) PEG 20000, 0.1 M BICINE pH 9, 0.5% (V/V) Dioxane
Crystal Properties
Matthews coefficientSolvent content
2.5351.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.085α = 90
b = 112.085β = 90
c = 249.949γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray213.15PIXELDECTRIS PILATUS3 X 2M2020-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.1819.81492.90.280.29980.10490.9886.197.6368945
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.182.32748.41.21991.3550.5820.5121.575.283448

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 REPLACEMENTTHROUGHOUT5UZU2.1819.8168945351382.40.20590.20380.2438RANDOM32.35
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]
0.01880.0188-0.0376
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion14.98
t_omega_torsion3.26
t_angle_deg0.98
t_bond_d0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_nbd
t_chiral_improper_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10274
Nucleic Acid Atoms
Solvent Atoms526
Heterogen Atoms372

Software

Software
Software NamePurpose
autoPROCdata processing
Aimlessdata scaling
STARANISOdata scaling
BUSTERrefinement
autoPROCdata reduction
PHASERphasing