6LKD

in meso full-length rat KMO in complex with a pyrazoyl benzoic acid inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4J33 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2930.04 M Tris-Cl pH 7.0, 0.06 M Bis-Tris pH 6.5, 0.3-0.51 M lithium sulfate, and 34-45 % PEG400
Crystal Properties
Matthews coefficientSolvent content
3.1666.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.97α = 90
b = 63.43β = 113.52
c = 152.42γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2017-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1.000SPring-8BL32XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1349.2599.80.990.9578.7722.82864135.055
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.1899.97.010.5331.222.7

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 REPLACEMENTTHROUGHOUT4J33349.2527209143299.950.22180.21970.2615RANDOM52.274
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]
0.040.02-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.202
r_dihedral_angle_3_deg21.332
r_dihedral_angle_4_deg19.396
r_dihedral_angle_1_deg7.618
r_angle_refined_deg1.741
r_angle_other_deg1.084
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.202
r_dihedral_angle_3_deg21.332
r_dihedral_angle_4_deg19.396
r_dihedral_angle_1_deg7.618
r_angle_refined_deg1.741
r_angle_other_deg1.084
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6778
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms180

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction