7PXV

LsAA9_A chemically reduced with ascorbic acid (high X-ray dose)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42983.5 M sodium chloride, 0.1 M citric acid pH 4.0 After the crystals were grown, they were transferred to a drop consisting of 3.5 M sodium chloride, 0.1 M citric acid pH 5.5, 0.01 M ascorbic acid pH 5.5 for 20 minutes before flash freezing
Crystal Properties
Matthews coefficientSolvent content
3.2562.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.41α = 90
b = 125.41β = 90
c = 125.41γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P110.97PETRA 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
11.544.381000.1620.99916.6520.4854321
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)
11.51.541002.7520.5972.2721.19

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 SYNTHESISTHROUGHOUT5ACH1.544.3851561275399.980.18840.18740.207RANDOM19.257
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_deg30.629
r_dihedral_angle_4_deg11.525
r_dihedral_angle_3_deg9.248
r_dihedral_angle_1_deg6.708
r_angle_refined_deg1.769
r_angle_other_deg1.427
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_refined0.012
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.629
r_dihedral_angle_4_deg11.525
r_dihedral_angle_3_deg9.248
r_dihedral_angle_1_deg6.708
r_angle_refined_deg1.769
r_angle_other_deg1.427
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1788
Nucleic Acid Atoms
Solvent Atoms269
Heterogen Atoms18

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing