7DSP

Anthranilate phosphoribosyltransferase variant Ser121Ala from Saccharomyces cerevisiae with Mg bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7DSM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP28718 % MPEG 5000, 0.1 M HEPES pH7.0
Crystal Properties
Matthews coefficientSolvent content
2.1843.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.164α = 90
b = 87.002β = 90
c = 108.433γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.97915SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.95501000.090.02532.21355409
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.981000.5170.1433.712.9

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 REPLACEMENTTHROUGHOUT7DSM1.9546.0652587272699.90.16570.16350.2079RANDOM29.652
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]
-0.121.19-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.418
r_dihedral_angle_3_deg15.902
r_dihedral_angle_4_deg14.359
r_dihedral_angle_1_deg6.323
r_angle_refined_deg1.493
r_angle_other_deg1.46
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.418
r_dihedral_angle_3_deg15.902
r_dihedral_angle_4_deg14.359
r_dihedral_angle_1_deg6.323
r_angle_refined_deg1.493
r_angle_other_deg1.46
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5473
Nucleic Acid Atoms
Solvent Atoms442
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing