5SYV

Crystal structure of Burkholderia pseudomallei KatG N240D variant


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29316-20% PEG 4000, 20% MPD, 0.1 M sodium citrate pH 5.6
Crystal Properties
Matthews coefficientSolvent content
3.1360.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.792α = 90
b = 113.296β = 90
c = 174.52γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.98CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.75174.5298.30.06915.13.9197628
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)
11.751.8499.90.4261.83.929084

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 REPLACEMENTTHROUGHOUT1MWV1.7548187721990798.350.16010.15850.1897RANDOM19.248
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]
-0.251.29-1.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.428
r_dihedral_angle_4_deg18.075
r_dihedral_angle_3_deg12.939
r_dihedral_angle_1_deg6.028
r_mcangle_it2.295
r_angle_refined_deg2.182
r_mcbond_it1.514
r_mcbond_other1.512
r_angle_other_deg1.255
r_chiral_restr0.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.428
r_dihedral_angle_4_deg18.075
r_dihedral_angle_3_deg12.939
r_dihedral_angle_1_deg6.028
r_mcangle_it2.295
r_angle_refined_deg2.182
r_mcbond_it1.514
r_mcbond_other1.512
r_angle_other_deg1.255
r_chiral_restr0.149
r_bond_refined_d0.026
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 Atoms11014
Nucleic Acid Atoms
Solvent Atoms1632
Heterogen Atoms139

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing