6HBS

Structure of PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BS8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.1 M HEPES, pH 7.0 0.1 M Ammonium Sulfate 30 % (w/v) Polyacrylate, sodium salt
Crystal Properties
Matthews coefficientSolvent content
2.141.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.18α = 90
b = 104.419β = 109.26
c = 65.25γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.6546.8399.560.0570.0680.03750.99912.43.295437
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.70999.090.67570.81820.45550.7121.573

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 REPLACEMENTTHROUGHOUT3BS81.6546.8390702473699.540.170990.169410.20189RANDOM24.866
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]
-0.39-0.211.09-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.863
r_dihedral_angle_4_deg16.798
r_dihedral_angle_3_deg13.583
r_dihedral_angle_1_deg6.659
r_long_range_B_refined5.469
r_long_range_B_other5.371
r_scangle_other4.274
r_scbond_it2.818
r_scbond_other2.817
r_mcangle_it2.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.863
r_dihedral_angle_4_deg16.798
r_dihedral_angle_3_deg13.583
r_dihedral_angle_1_deg6.659
r_long_range_B_refined5.469
r_long_range_B_other5.371
r_scangle_other4.274
r_scbond_it2.818
r_scbond_other2.817
r_mcangle_it2.246
r_mcangle_other2.246
r_mcbond_it1.646
r_mcbond_other1.644
r_angle_refined_deg1.391
r_angle_other_deg0.987
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
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 Atoms6394
Nucleic Acid Atoms
Solvent Atoms587
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing