1PQE

S25A mutant of pyruvoyl dependent aspartate decarboxylase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AW8PDB entry 1aw8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8292NH42SO4,Tris/HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.957.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.056α = 90
b = 73.056β = 90
c = 111.114γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors1999-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.953095.20.0436.69.311321326.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0292.70.3284.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1aw81.9524.5113211024451895.130.160320.160320.158040.20492RANDOM7.708
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]
0.220.22-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.752
r_scangle_it2.205
r_scbond_it1.632
r_angle_refined_deg1.486
r_mcangle_it0.904
r_angle_other_deg0.789
r_mcbond_it0.602
r_symmetry_vdw_other0.32
r_nbd_other0.262
r_nbd_refined0.215
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.752
r_scangle_it2.205
r_scbond_it1.632
r_angle_refined_deg1.486
r_mcangle_it0.904
r_angle_other_deg0.789
r_mcbond_it0.602
r_symmetry_vdw_other0.32
r_nbd_other0.262
r_nbd_refined0.215
r_xyhbond_nbd_refined0.188
r_symmetry_hbond_refined0.181
r_symmetry_vdw_refined0.143
r_chiral_restr0.092
r_nbtor_other0.086
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_gen_planes_other0.005
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms894
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing