1PYU

Processed Aspartate Decarboxylase Mutant with Ser25 mutated to Cys


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42900.1M citric acid, 1.6M ammonium sulphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.550.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.787α = 90
b = 70.787β = 90
c = 217.121γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOsmic Confocal MaxFlux optic system2003-03-10MSINGLE 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
11.93098.70.08228.312.626051253222231.7
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)
11.91.9288.30.3233.011767

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)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 1aw81.93022605124733132598.620.173790.172560.19614RANDOM19.04
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]
0.540.270.54-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.168
r_scangle_it3.029
r_scbond_it1.921
r_angle_refined_deg1.417
r_angle_other_deg1.153
r_mcangle_it1.148
r_mcbond_it0.636
r_symmetry_vdw_other0.341
r_symmetry_hbond_refined0.272
r_xyhbond_nbd_refined0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.168
r_scangle_it3.029
r_scbond_it1.921
r_angle_refined_deg1.417
r_angle_other_deg1.153
r_mcangle_it1.148
r_mcbond_it0.636
r_symmetry_vdw_other0.341
r_symmetry_hbond_refined0.272
r_xyhbond_nbd_refined0.27
r_nbd_other0.253
r_nbd_refined0.227
r_symmetry_vdw_refined0.199
r_chiral_restr0.115
r_nbtor_other0.087
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1777
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing