2VEG

Dihydropteroate synthase from Streptococcus pneumoniae: complex with 6-hydroxymethyl-7,8-dihydropterin monophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VEFPDB ENTRY 2VEF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2 M AMMONIUM IODIDE AND 20% (W/V) POLYETHYLENE GLYCOL 3,350
Crystal Properties
Matthews coefficientSolvent content
2.244.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.653α = 90
b = 90.617β = 90
c = 136.602γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEOSMICMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
12.468.383.50.0615.24.57191243
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)
12.42.4941.80.293.22.22

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2VEF2.4201809597583.50.220.2160.297RANDOM36.88
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]
5.66-3.03-2.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.314
r_dihedral_angle_4_deg18.668
r_dihedral_angle_3_deg18.594
r_dihedral_angle_1_deg6.485
r_scangle_it3.597
r_scbond_it2.19
r_angle_refined_deg1.618
r_mcangle_it1.343
r_mcbond_it1.218
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.314
r_dihedral_angle_4_deg18.668
r_dihedral_angle_3_deg18.594
r_dihedral_angle_1_deg6.485
r_scangle_it3.597
r_scbond_it2.19
r_angle_refined_deg1.618
r_mcangle_it1.343
r_mcbond_it1.218
r_nbtor_refined0.302
r_symmetry_hbond_refined0.289
r_symmetry_vdw_refined0.236
r_nbd_refined0.224
r_xyhbond_nbd_refined0.174
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4271
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing