6RTS

Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus complexed with NAD+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6RTR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52930,1 M sodium acetate pH 5, 2.2 M ammonium sulphate, 0.2 M lithium acetate
Crystal Properties
Matthews coefficientSolvent content
2.6854.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.04α = 90
b = 131.24β = 90
c = 157.71γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.2545.499.40.1598.323.75452221.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3199.80.6632.223.8

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 REPLACEMENTTHROUGHOUT6RTR2.2545.451800272799.390.167520.165550.20467RANDOM23.13
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]
0.81-0.33-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.442
r_dihedral_angle_4_deg16.845
r_dihedral_angle_3_deg12.831
r_dihedral_angle_1_deg6.106
r_long_range_B_refined4.995
r_long_range_B_other4.912
r_scangle_other3.241
r_mcangle_it2.025
r_mcangle_other2.025
r_scbond_it1.975
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.442
r_dihedral_angle_4_deg16.845
r_dihedral_angle_3_deg12.831
r_dihedral_angle_1_deg6.106
r_long_range_B_refined4.995
r_long_range_B_other4.912
r_scangle_other3.241
r_mcangle_it2.025
r_mcangle_other2.025
r_scbond_it1.975
r_scbond_other1.975
r_angle_refined_deg1.47
r_mcbond_it1.233
r_mcbond_other1.231
r_angle_other_deg1.007
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms7541
Nucleic Acid Atoms
Solvent Atoms543
Heterogen Atoms170

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing