5MSO

Structure of the R domain of carboxylic acid reductase (CAR) from Mycobacterium marinum in complex with NADP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277Co-crystals of CARmm Red domain with NADP were obtained in 0.2 M sodium sulphate, 0.1 M Bis-Tris-propane pH 6.5, 20% PEG3350

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.242α = 90
b = 136.156β = 90
c = 115.488γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.2115.49990.041183.9143907
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.241000.5

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 REPLACEMENTTHROUGHOUT4DQV1.2115.49136673723494.280.135730.134860.15198RANDOM21.396
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]
-0.130.040.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.021
r_sphericity_free27.695
r_dihedral_angle_4_deg18.604
r_sphericity_bonded10.277
r_dihedral_angle_3_deg10.147
r_dihedral_angle_1_deg5.847
r_long_range_B_refined3.156
r_long_range_B_other3.156
r_scangle_other2.345
r_rigid_bond_restr2.061
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.021
r_sphericity_free27.695
r_dihedral_angle_4_deg18.604
r_sphericity_bonded10.277
r_dihedral_angle_3_deg10.147
r_dihedral_angle_1_deg5.847
r_long_range_B_refined3.156
r_long_range_B_other3.156
r_scangle_other2.345
r_rigid_bond_restr2.061
r_scbond_it1.842
r_scbond_other1.842
r_mcangle_it1.796
r_mcangle_other1.796
r_angle_refined_deg1.587
r_mcbond_it1.407
r_mcbond_other1.396
r_angle_other_deg0.989
r_chiral_restr0.098
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3400
Nucleic Acid Atoms
Solvent Atoms475
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing