5MSP

Structure of the unmodified PCP-R didomain of carboxylic acid reductase (CAR) from Segniliparus rugosus in complex with NADP, F2221 form


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 sodium malonate dibasic monohydrate, 0.1 M HEPES pH 7.0, 0.5% Jeffamine ED-2003.

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.37α = 90
b = 137.68β = 90
c = 202.08γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-07-19MSINGLE 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
12.41101.04990.11185.436214
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)
12.412.599.50.6

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 REPLACEMENTTHROUGHOUT5MSO2.41101.0434488172899.240.181170.178940.22697RANDOM66.76
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]
6.26-1.95-4.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.685
r_dihedral_angle_4_deg20.761
r_dihedral_angle_3_deg17.774
r_long_range_B_refined12.018
r_long_range_B_other12.016
r_scangle_other10.015
r_mcangle_it7.48
r_mcangle_other7.479
r_scbond_other6.591
r_scbond_it6.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.685
r_dihedral_angle_4_deg20.761
r_dihedral_angle_3_deg17.774
r_long_range_B_refined12.018
r_long_range_B_other12.016
r_scangle_other10.015
r_mcangle_it7.48
r_mcangle_other7.479
r_scbond_other6.591
r_scbond_it6.59
r_dihedral_angle_1_deg6.555
r_mcbond_it5.346
r_mcbond_other5.346
r_angle_refined_deg1.912
r_angle_other_deg1.116
r_chiral_restr0.118
r_bond_refined_d0.017
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3911
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing