7YHE

Crystal structure of the triple mutant CmnC-L136Q,S138G,D249Y in complex with alpha-KG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WBO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529320 mM ammonium acetate, 24% v/v polyethylene glycol 400, 0.1 M sodium citrate tribasic dihydrate
Crystal Properties
Matthews coefficientSolvent content
2.6353.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.115α = 90
b = 127.191β = 90
c = 138.759γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDRAYONIX MX300-HS2021-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.673099.90.05524.054.595108
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)
11.671.731000.760.7572.024.4

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 REPLACEMENTTHROUGHOUT2WBO1.6727.6785445453394.350.17880.1780.1936RANDOM16.668
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]
-0.16-0.150.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.106
r_dihedral_angle_4_deg16.537
r_dihedral_angle_3_deg12.434
r_dihedral_angle_1_deg6.928
r_angle_other_deg1.324
r_angle_refined_deg1.279
r_chiral_restr0.06
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.106
r_dihedral_angle_4_deg16.537
r_dihedral_angle_3_deg12.434
r_dihedral_angle_1_deg6.928
r_angle_other_deg1.324
r_angle_refined_deg1.279
r_chiral_restr0.06
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5228
Nucleic Acid Atoms
Solvent Atoms512
Heterogen Atoms31

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing