5GJM

Crystal structure of Lysine decarboxylase from Selenomonas ruminantium in C2 space group


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293Sodium citrate, Sodium cacodylate
Crystal Properties
Matthews coefficientSolvent content
2.5952.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.45α = 90
b = 70.794β = 101.03
c = 88.061γ = 90
Symmetry
Space GroupC 1 2 1

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)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
12.95095.20.14517.23.518678
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.9594.20.3460.673.3

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 REPLACEMENTTHROUGHOUT2PLJ2.91501774893094.680.181250.177160.23364RANDOM21.219
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]
-1.290.33.2-1.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.094
r_dihedral_angle_3_deg18.497
r_dihedral_angle_4_deg17.266
r_dihedral_angle_1_deg7.299
r_long_range_B_refined4.501
r_long_range_B_other4.501
r_mcangle_it2.45
r_mcangle_other2.45
r_scangle_other2.403
r_angle_refined_deg1.704
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.094
r_dihedral_angle_3_deg18.497
r_dihedral_angle_4_deg17.266
r_dihedral_angle_1_deg7.299
r_long_range_B_refined4.501
r_long_range_B_other4.501
r_mcangle_it2.45
r_mcangle_other2.45
r_scangle_other2.403
r_angle_refined_deg1.704
r_scbond_it1.38
r_scbond_other1.38
r_mcbond_it1.374
r_mcbond_other1.374
r_angle_other_deg1.024
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5785
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACTdata extraction