5VIS

1.73 Angstrom Resolution Crystal Structure of Dihydropteroate Synthase (folP-SMZ_B27) from Soil Uncultured Bacterium.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AJ2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5295Protein: 30.0 mg/ml, 0.25M Sodium chloride, 0.25M Potassium chloride, 0.01M HEPES (pH 7.5); Screen: 0.2M Potassium citrate, 0.1M MES (pH 6.5), 20% (w/v) PEG 3350; Cryo: 5% (v/v) PEG 200, paratone.
Crystal Properties
Matthews coefficientSolvent content
2.252.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.822α = 90
b = 101.822β = 90
c = 206.137γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2017-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rpim 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
11.733099.90.0720.0720.03120.7666663-321.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.761000.7520.7520.3250.7372.65.9

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 REPLACEMENTTHROUGHOUT1AJ21.7329.9963061334699.840.15830.156610.19091RANDOM24.277
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]
-0.23-0.12-0.230.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.249
r_dihedral_angle_4_deg14.279
r_dihedral_angle_3_deg8.302
r_long_range_B_refined6.188
r_long_range_B_other5.836
r_dihedral_angle_1_deg2.645
r_scangle_other2.607
r_mcangle_it1.915
r_mcangle_other1.915
r_scbond_it1.631
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.249
r_dihedral_angle_4_deg14.279
r_dihedral_angle_3_deg8.302
r_long_range_B_refined6.188
r_long_range_B_other5.836
r_dihedral_angle_1_deg2.645
r_scangle_other2.607
r_mcangle_it1.915
r_mcangle_other1.915
r_scbond_it1.631
r_scbond_other1.629
r_angle_refined_deg1.471
r_mcbond_it1.158
r_mcbond_other1.156
r_angle_other_deg0.879
r_chiral_restr0.094
r_gen_planes_refined0.023
r_gen_planes_other0.02
r_bond_refined_d0.009
r_bond_other_d0.001
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 Atoms4113
Nucleic Acid Atoms
Solvent Atoms630
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing