7Y5P

Crystal structure of CmnC in complex with L-arginine and alpha-KG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7VGL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.2M Ammonium acetate, 0.1M Na citrate tribasic dihydrate pH 5.5, 24% v/v Polyethylene glycol 400
Crystal Properties
Matthews coefficientSolvent content
2.7855.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.998α = 90
b = 127.292β = 90
c = 139.019γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2022-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A10.9732NSRRCBL15A1

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
11.73099.70.05527.565.590120
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)
11.71.761000.6042.42

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 REPLACEMENTTHROUGHOUT7VGL1.726.2882573438495.940.17880.17750.2036RANDOM17.297
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]
-0.13-0.040.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.91
r_dihedral_angle_4_deg15.444
r_dihedral_angle_3_deg12.536
r_dihedral_angle_1_deg6.935
r_angle_other_deg1.32
r_angle_refined_deg1.291
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.91
r_dihedral_angle_4_deg15.444
r_dihedral_angle_3_deg12.536
r_dihedral_angle_1_deg6.935
r_angle_other_deg1.32
r_angle_refined_deg1.291
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5222
Nucleic Acid Atoms
Solvent Atoms503
Heterogen Atoms33

Software

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