X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LYC5LYC chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29324 % PEG 3350 0.27 M NaCl 0.09 M MES pH 5.5 (2x protein solution : 1x crystallisation condition)
Crystal Properties
Matthews coefficientSolvent content
3.8167.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.68α = 90
b = 66.68β = 90
c = 142.881γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2017-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.980SOLEILPROXIMA 2

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
12.571.4499.70.1310.1580.0860.9845.73.124569
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)
12.52.699.90.390.470.2590.6073.1

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 REPLACEMENTTHROUGHOUT5LYC chain A2.557.7523441109099.750.17720.17610.1998RANDOM41.858
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]
13.9813.98-27.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.034
r_dihedral_angle_4_deg21.613
r_dihedral_angle_3_deg12.728
r_dihedral_angle_1_deg6.04
r_angle_refined_deg1.375
r_angle_other_deg0.903
r_chiral_restr0.09
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.034
r_dihedral_angle_4_deg21.613
r_dihedral_angle_3_deg12.728
r_dihedral_angle_1_deg6.04
r_angle_refined_deg1.375
r_angle_other_deg0.903
r_chiral_restr0.09
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3384
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms497

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction