5MSR

Structure of the unmodified PCP-R domain of carboxylic acid reductase (CAR) from Segniliparus rugosus in complex with NADPH, P43 form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277CARsr PCP-Red crystals were obtained in the condition 0.1 M sodium malonate dibasic monohydrate, 0.1 M HEPES pH 7.0, 0.5% Jeffamine ED-2003.

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.943α = 90
b = 94.943β = 90
c = 335.506γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-07-16MSINGLE 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
12.37200990.1316.45.6112379
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)
12.372.4699.50.5

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 REPLACEMENTTHROUGHOUT5MSO2.37200112379566798.650.21980.218690.24127RANDOM86.534
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]
0.020.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.895
r_dihedral_angle_4_deg15.368
r_dihedral_angle_3_deg15.037
r_long_range_B_refined10.575
r_long_range_B_other10.575
r_scangle_other7.86
r_mcangle_it6.949
r_mcangle_other6.948
r_dihedral_angle_1_deg5.152
r_scbond_other5.054
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.895
r_dihedral_angle_4_deg15.368
r_dihedral_angle_3_deg15.037
r_long_range_B_refined10.575
r_long_range_B_other10.575
r_scangle_other7.86
r_mcangle_it6.949
r_mcangle_other6.948
r_dihedral_angle_1_deg5.152
r_scbond_other5.054
r_scbond_it5.053
r_mcbond_it4.662
r_mcbond_other4.661
r_angle_refined_deg1.337
r_angle_other_deg1.258
r_chiral_restr0.08
r_bond_refined_d0.008
r_bond_other_d0.004
r_gen_planes_refined0.004
r_gen_planes_other0.003
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 Atoms15712
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing