5MSW

Structure of the A-PCP didomain of carboxylic acid reductase (CAR) from Segniliparus rugosus in complex with AMP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277A-PCP crystals were obtained in 0.2 M sodium fluoride, 0.1 M Bis-Tris Propane pH 6.5 and 20% PEG3350.

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.42α = 90
b = 65.33β = 110.8
c = 101.71γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-07-20MSINGLE 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
12.3395.08990.09110.92.834371
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)
12.332.410.5

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 REPLACEMENTTHROUGHOUT5MSQ2.3395.0832634173899.050.196020.193520.24337RANDOM47.076
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]
1.060.33-2.430.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.561
r_dihedral_angle_4_deg20.382
r_dihedral_angle_3_deg17.473
r_long_range_B_other8.494
r_long_range_B_refined8.489
r_dihedral_angle_1_deg6.754
r_scangle_other6.506
r_mcangle_it5.198
r_mcangle_other5.198
r_scbond_it4.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.561
r_dihedral_angle_4_deg20.382
r_dihedral_angle_3_deg17.473
r_long_range_B_other8.494
r_long_range_B_refined8.489
r_dihedral_angle_1_deg6.754
r_scangle_other6.506
r_mcangle_it5.198
r_mcangle_other5.198
r_scbond_it4.123
r_scbond_other4.122
r_mcbond_it3.501
r_mcbond_other3.498
r_angle_refined_deg1.717
r_angle_other_deg1.035
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_refined0.007
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5431
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing