6QP1

Crystal structure of the PLP-bound C-S lyase in the external aldimine form from Staphylococcus hominis complexed with an inhibitor, L-cycloserine.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DQ6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298.154% Tacsimate pH 6.0, 12% PEG 3,350 (F1: PEG/ION HT, Hampton Research), 20mM L-cycloserine
Crystal Properties
Matthews coefficientSolvent content
1.9737.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.466α = 90
b = 115.456β = 90
c = 118.962γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS3 6M2018-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.4252.8899.60.1030.110.0390.9979.87.9143873
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.421.4499.12.5032.6730.9290.3318

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 REPLACEMENTTHROUGHOUT4DQ61.4251.99136702708599.50.19210.19070.2189RANDOM22.723
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]
0.081.11-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.198
r_dihedral_angle_4_deg16.51
r_dihedral_angle_3_deg13.608
r_dihedral_angle_1_deg7.169
r_angle_refined_deg1.625
r_angle_other_deg1.057
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.198
r_dihedral_angle_4_deg16.51
r_dihedral_angle_3_deg13.608
r_dihedral_angle_1_deg7.169
r_angle_refined_deg1.625
r_angle_other_deg1.057
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6341
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms44

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing