1PT0

Unprocessed Pyruvoyl Dependent Aspartate Decarboxylase with an Alanine insertion at position 26


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
2.550.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.935α = 90
b = 70.935β = 90
c = 217.741γ = 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
122599.70.06437.5423.72301322903223.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0599.30.1910.1071256.6

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 1AW82202301321139166999.620.175190.175190.173940.19084RANDOM10.47
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]
-0.04-0.02-0.040.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.201
r_scangle_it3.835
r_scbond_it2.283
r_angle_refined_deg1.469
r_mcangle_it1.349
r_angle_other_deg1.106
r_mcbond_it0.731
r_symmetry_vdw_other0.32
r_nbd_other0.257
r_symmetry_hbond_refined0.245
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.201
r_scangle_it3.835
r_scbond_it2.283
r_angle_refined_deg1.469
r_mcangle_it1.349
r_angle_other_deg1.106
r_mcbond_it0.731
r_symmetry_vdw_other0.32
r_nbd_other0.257
r_symmetry_hbond_refined0.245
r_nbd_refined0.203
r_xyhbond_nbd_refined0.175
r_symmetry_vdw_refined0.15
r_chiral_restr0.135
r_nbtor_other0.086
r_bond_refined_d0.015
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 Atoms1743
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing