7NIM

X-ray crystal structure of LsAA9A - cinnamon extract soak


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42953.5 M NaCl, 0.1 M citric acid pH 4.0. 20-25 mg/ml LsAA9A. 2 ul hanging drops (1:1 protein:reservoir ratio).
Crystal Properties
Matthews coefficientSolvent content
3.2361.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.179α = 90
b = 125.179β = 90
c = 125.179γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0332PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.4544.31000.1650.99920.5770.159727
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.5499.81.8460.7141.3

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5ACH1.4544.356643300999.980.16830.16720.1873RANDOM21.047
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.535
r_dihedral_angle_4_deg11.84
r_dihedral_angle_3_deg8.61
r_dihedral_angle_1_deg6.851
r_angle_refined_deg2.083
r_angle_other_deg1.584
r_chiral_restr0.133
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.535
r_dihedral_angle_4_deg11.84
r_dihedral_angle_3_deg8.61
r_dihedral_angle_1_deg6.851
r_angle_refined_deg2.083
r_angle_other_deg1.584
r_chiral_restr0.133
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1788
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms148

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction