3N2B

1.8 Angstrom Resolution Crystal Structure of Diaminopimelate Decarboxylase (lysA) from Vibrio cholerae.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P3E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8295Protein solution: 7.8 mg/mL, 0.25M Sodium chloride, 0.01M Tris pH 8.3; Screen solution: PACT (D8) 0.2M Ammonium chloride, 0.1M Tris pH 8.0, 20%(w/v) PEG6000., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1242.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.394α = 105.31
b = 80.329β = 93.62
c = 118.693γ = 90.52
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium lenses2010-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.83097.50.04817.42.6147832147832-328.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8396.20.3632.72.67354

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 REPLACEMENTTHROUGHOUT2P3E1.829.94138491138491728997.510.184490.184490.182660.21874RANDOM31.855
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]
1.510.34-0.25-2.98-1.490.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.451
r_dihedral_angle_4_deg13.373
r_dihedral_angle_3_deg9.495
r_scangle_it4.63
r_dihedral_angle_1_deg3.243
r_scbond_it2.928
r_mcangle_it2.072
r_angle_refined_deg1.392
r_mcbond_it1.214
r_angle_other_deg0.846
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.451
r_dihedral_angle_4_deg13.373
r_dihedral_angle_3_deg9.495
r_scangle_it4.63
r_dihedral_angle_1_deg3.243
r_scbond_it2.928
r_mcangle_it2.072
r_angle_refined_deg1.392
r_mcbond_it1.214
r_angle_other_deg0.846
r_mcbond_other0.327
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12599
Nucleic Acid Atoms
Solvent Atoms1121
Heterogen Atoms4

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling