6PZ2

Crystal Structure of FolP (dihydropteroate synthase) from Colstridium difficile in the presence of pteroic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HB7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92932.4-2.6 M ammonium sulfate, 200 mM LiCl, 100 mM CHES (pH 9), 4 mM pteroic acid
Crystal Properties
Matthews coefficientSolvent content
5.0175.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 156.258α = 90
b = 156.258β = 90
c = 84.708γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2018-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.99861APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
125099.20.09845.41341365
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0399.50.4544.37.7

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4hb7237.5639244211698.930.18950.18760.2238RANDOM39.817
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]
-1.63-0.81-1.635.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.698
r_dihedral_angle_3_deg15.964
r_dihedral_angle_4_deg15.207
r_dihedral_angle_1_deg6.493
r_angle_refined_deg1.753
r_angle_other_deg0.549
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.698
r_dihedral_angle_3_deg15.964
r_dihedral_angle_4_deg15.207
r_dihedral_angle_1_deg6.493
r_angle_refined_deg1.753
r_angle_other_deg0.549
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2061
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing