6NBP | pdb_00006nbp

Crystal Structure of a Sugar N-Formyltransferase from the Plant Pathogen Pantoea ananatis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YFV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829513-16%PEG-3350, 2 mM folinic acid, 5 mM dTDP-Qui4N, 200 mM NaCl, 100 mM HEPES
Crystal Properties
Matthews coefficientSolvent content
2.4349.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.928α = 90
b = 75.928β = 90
c = 87.591γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352018-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.75098.30.0610.06113.17.632264
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.894.10.4330.4332.13.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4YFV1.75030727153798.290.187640.185740.190.226460.23RANDOM26.513
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]
0.480.240.48-1.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.091
r_dihedral_angle_4_deg21.798
r_dihedral_angle_3_deg16.251
r_dihedral_angle_1_deg6.786
r_long_range_B_refined6.407
r_long_range_B_other6.312
r_scangle_other4.395
r_mcangle_it3.39
r_mcangle_other3.388
r_scbond_it2.875
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.091
r_dihedral_angle_4_deg21.798
r_dihedral_angle_3_deg16.251
r_dihedral_angle_1_deg6.786
r_long_range_B_refined6.407
r_long_range_B_other6.312
r_scangle_other4.395
r_mcangle_it3.39
r_mcangle_other3.388
r_scbond_it2.875
r_scbond_other2.82
r_mcbond_it2.248
r_mcbond_other2.247
r_angle_refined_deg1.554
r_angle_other_deg0.504
r_chiral_restr0.068
r_bond_refined_d0.011
r_gen_planes_refined0.009
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 Atoms1966
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing