6HBV

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 DROP29830 % w/v Polyactulate 2100, sodium salt 0.2 M Ammonium Sulfate 0.1 M Hepes pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.0941.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.254α = 90
b = 103.903β = 109.61
c = 65.326γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.98DiamondI04

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
11.6546.8699.740.062150.072640.037150.99913.953.795210
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)
11.651.70999.730.55540.65210.33710.8492.193.6

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 REPLACEMENTTHROUGHOUT3bs81.6546.9191044476499.520.144370.142810.17414RANDOM20.583
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]
-1.49-0.763.69-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.72
r_dihedral_angle_1_deg18.15
r_dihedral_angle_4_deg17.542
r_dihedral_angle_3_deg13.286
r_long_range_B_refined5.598
r_long_range_B_other5.261
r_scangle_other4.14
r_scbond_it2.721
r_scbond_other2.721
r_mcangle_it1.864
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.72
r_dihedral_angle_1_deg18.15
r_dihedral_angle_4_deg17.542
r_dihedral_angle_3_deg13.286
r_long_range_B_refined5.598
r_long_range_B_other5.261
r_scangle_other4.14
r_scbond_it2.721
r_scbond_other2.721
r_mcangle_it1.864
r_mcangle_other1.864
r_angle_refined_deg1.56
r_mcbond_it1.387
r_mcbond_other1.376
r_angle_other_deg1.062
r_chiral_restr0.088
r_bond_refined_d0.012
r_bond_other_d0.001
r_gen_planes_refined0.001
r_gen_planes_other
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 Atoms6386
Nucleic Acid Atoms
Solvent Atoms944
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing