5MSV

Structure of the phosphopantetheine modified PCP-R didomain of carboxylic acid reductase (CAR) in complex with NADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MSO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277CARsr PCP-Red crystals were obtained in 0.1 M carboxylic acids 0.1M, Buffer system 1 pH 6.5, 50% Precipitant Mix 2 of Morpheus screen.

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.11α = 90
b = 92.11β = 90
c = 363.5γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-10-04MSINGLE 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
12.34200950.12111.36.8120649
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)
12.342.4292.30.5

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 REPLACEMENTTHROUGHOUT5MSO2.34200114730592395.240.192230.191430.2075RANDOM44.473
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]
-0.53-0.531.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.422
r_dihedral_angle_4_deg15.607
r_dihedral_angle_3_deg14.759
r_long_range_B_refined6.481
r_long_range_B_other6.48
r_dihedral_angle_1_deg5.282
r_scangle_other5.148
r_mcangle_it3.529
r_mcangle_other3.529
r_scbond_it3.283
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.422
r_dihedral_angle_4_deg15.607
r_dihedral_angle_3_deg14.759
r_long_range_B_refined6.481
r_long_range_B_other6.48
r_dihedral_angle_1_deg5.282
r_scangle_other5.148
r_mcangle_it3.529
r_mcangle_other3.529
r_scbond_it3.283
r_scbond_other3.283
r_mcbond_it2.349
r_mcbond_other2.348
r_angle_refined_deg1.367
r_angle_other_deg1.269
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.004
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15747
Nucleic Acid Atoms
Solvent Atoms790
Heterogen Atoms244

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing