1PT1

Unprocessed Pyruvoyl Dependent Aspartate Decarboxylase with Histidine 11 Mutated to Alanine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42901.4-1.6M Ammonium Sulphate, 0.1M Citric Acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.550.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.952α = 90
b = 70.952β = 90
c = 217.081γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.11.488SRSPX14.1

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
11.9251000.08731.2333.52655726521216.1
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)
11.91.941000.269.79

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 1aw81.923.442655724507192899.870.150050.150050.148470.16963RANDOM7.41
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]
-0.03-0.01-0.030.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.659
r_scangle_it3.572
r_scbond_it2.719
r_angle_refined_deg1.35
r_mcangle_it1.221
r_angle_other_deg0.77
r_mcbond_it0.651
r_symmetry_vdw_other0.365
r_nbd_other0.263
r_symmetry_hbond_refined0.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.659
r_scangle_it3.572
r_scbond_it2.719
r_angle_refined_deg1.35
r_mcangle_it1.221
r_angle_other_deg0.77
r_mcbond_it0.651
r_symmetry_vdw_other0.365
r_nbd_other0.263
r_symmetry_hbond_refined0.225
r_nbd_refined0.22
r_symmetry_vdw_refined0.19
r_xyhbond_nbd_refined0.183
r_chiral_restr0.09
r_nbtor_other0.084
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_gen_planes_other0.005
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1774
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing