5X7N

Crystal structure of meso-diaminopimelate decarboxylase (DAPDC) from Corynebacterium glutamicum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5X7M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Sodium citrate tribasic, Sodium cacodylate
Crystal Properties
Matthews coefficientSolvent content
2.6553.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.543α = 90
b = 91.702β = 90
c = 95.161γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702014-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.97934PAL/PLS7A (6B, 6C1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7295.1795.240.235.995643
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.75

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5X7M1.7223.46195643505894.550.17250.17050.2112RANDOM18.718
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]
-0.19-0.360.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.196
r_dihedral_angle_4_deg11.914
r_dihedral_angle_3_deg10.981
r_dihedral_angle_1_deg6.301
r_angle_refined_deg2.124
r_angle_other_deg1.099
r_chiral_restr0.14
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.196
r_dihedral_angle_4_deg11.914
r_dihedral_angle_3_deg10.981
r_dihedral_angle_1_deg6.301
r_angle_refined_deg2.124
r_angle_other_deg1.099
r_chiral_restr0.14
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6618
Nucleic Acid Atoms
Solvent Atoms892
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing