6X7M

LnmK in complex with 2-nitronate-propionyl-oxa(dethia)-CoA


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2981.75 M ammonium sulfate, 33 mM HEPES pH 7.0, 67 mM HEPES 8.0, 9% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.3547.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.55α = 90
b = 61.55β = 90
c = 308.805γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80IMAGE PLATEMAR scanner 300 mm plateMD2 microdifractometer2016-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.615099.70.0810.0710.0830.020.99887.3204646533.892
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.611.6799.5110.9990.3490.8321.516.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4HZO1.6147.3844066230499.730.19180.190.2266RANDOM33.892
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]
0.830.420.83-2.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.052
r_dihedral_angle_4_deg15.816
r_dihedral_angle_3_deg13.86
r_dihedral_angle_1_deg7.178
r_angle_refined_deg1.989
r_angle_other_deg1.732
r_chiral_restr0.155
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.052
r_dihedral_angle_4_deg15.816
r_dihedral_angle_3_deg13.86
r_dihedral_angle_1_deg7.178
r_angle_refined_deg1.989
r_angle_other_deg1.732
r_chiral_restr0.155
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2366
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms98

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing
DENZOdata reduction