2BMB

X-ray structure of the bifunctional 6-hydroxymethyl-7,8- dihydroxypterin pyrophosphokinase dihydropteroate synthase from Saccharomyces cerevisiae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EYEPDB ENTRY 1EYE, PDB ENTRY 1CBK
experimental modelPDB 1CBKPDB ENTRY 1EYE, PDB ENTRY 1CBK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.51.17 M NAH2PO4, 0.63 M K2HPO4, PH 6.3
Crystal Properties
Matthews coefficientSolvent content
3.4463.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.566α = 90
b = 92.566β = 90
c = 192.401γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU IMAGE PLATEAXCO MONOCAPILLARY OPTICS2003-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
12.34099.10.1722.410.737688
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)
12.32.3491.10.853.82

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 1EYE, PDB ENTRY 1CBK2.34035738187799.10.180.1780.216RANDOM32.76
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]
-0.13-0.130.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.942
r_dihedral_angle_4_deg19.109
r_dihedral_angle_3_deg15.776
r_dihedral_angle_1_deg5.77
r_scangle_it5.433
r_mcangle_it4.402
r_scbond_it3.883
r_mcbond_it3.111
r_angle_refined_deg1.212
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.942
r_dihedral_angle_4_deg19.109
r_dihedral_angle_3_deg15.776
r_dihedral_angle_1_deg5.77
r_scangle_it5.433
r_mcangle_it4.402
r_scbond_it3.883
r_mcbond_it3.111
r_angle_refined_deg1.212
r_nbtor_refined0.299
r_nbd_refined0.197
r_symmetry_vdw_refined0.174
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.127
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms4094
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing