8ZXU | pdb_00008zxu

Crystal structure of N terminal deletion mutant of Staphylococcal atypical two-cysteine thiol peroxidase complexed with substrate analog


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PSQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298Ammonium sulfate, HEPES, PEG400
Crystal Properties
Matthews coefficientSolvent content
3.1561.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.267α = 90
b = 148.331β = 90
c = 72.952γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2024-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONRRCAT INDUS-2 BEAMLINE PX-BL210.978930RRCAT INDUS-2PX-BL21

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
11.5540.9395.70.0730.0870.0460.99493.6112790
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)
11.551.6393.40.2390.2780.1420.933.8

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)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1PSQ1.5540.93107108563595.590.164190.162540.1530.195030.1832RANDOM20.422
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]
-7.19-0.053.323.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.734
r_dihedral_angle_3_deg15.78
r_dihedral_angle_4_deg14.892
r_dihedral_angle_1_deg8.168
r_long_range_B_refined5.727
r_long_range_B_other5.564
r_scangle_other3.063
r_mcangle_it2.666
r_mcangle_other2.666
r_angle_refined_deg2.291
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.734
r_dihedral_angle_3_deg15.78
r_dihedral_angle_4_deg14.892
r_dihedral_angle_1_deg8.168
r_long_range_B_refined5.727
r_long_range_B_other5.564
r_scangle_other3.063
r_mcangle_it2.666
r_mcangle_other2.666
r_angle_refined_deg2.291
r_scbond_it2.189
r_scbond_other2.189
r_mcbond_it1.855
r_mcbond_other1.855
r_angle_other_deg0.779
r_chiral_restr0.128
r_bond_refined_d0.018
r_gen_planes_refined0.016
r_bond_other_d0.001
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 Atoms4616
Nucleic Acid Atoms
Solvent Atoms675
Heterogen Atoms149

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing