5TXQ

Crystal structure of the A143D variant of catalase-peroxidase from B. pseudomallei


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MWVPDBID 1MWV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.129320% MPD, 0.1 M sodium citrate, 17% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
3.2462.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.67α = 90
b = 115.117β = 90
c = 174.738γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2016-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.9795CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim 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
11.996.13199.80.0770.0860.03817.55159525159525
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9299.60.5631.45

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 REPLACEMENTTHROUGHOUTPDBID 1MWV1.996.13151540789999.720.15840.15660.1907RANDOM26.768
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]
-1.12.67-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.252
r_dihedral_angle_4_deg16.877
r_dihedral_angle_3_deg13.659
r_dihedral_angle_1_deg6.289
r_mcangle_it2.731
r_angle_refined_deg2.221
r_mcbond_it1.858
r_mcbond_other1.848
r_angle_other_deg1.18
r_chiral_restr0.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.252
r_dihedral_angle_4_deg16.877
r_dihedral_angle_3_deg13.659
r_dihedral_angle_1_deg6.289
r_mcangle_it2.731
r_angle_refined_deg2.221
r_mcbond_it1.858
r_mcbond_other1.848
r_angle_other_deg1.18
r_chiral_restr0.154
r_bond_refined_d0.027
r_gen_planes_refined0.015
r_gen_planes_other0.01
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11020
Nucleic Acid Atoms
Solvent Atoms1490
Heterogen Atoms118

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction