7PXT

Structure of an LPMO, collected from serial synchrotron crystallography data.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42984.1 M NaCl, 0.1 M citric acid pH 4.0 The crystals were equilibrated in a drop of 3.5 M NaCl, 0.1 M citric acid pH 5.5
Crystal Properties
Matthews coefficientSolvent content
3.2562.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.42α = 90
b = 125.42β = 90
c = 125.42γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI JUNGFRAU 4M2017-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.98ESRFID29

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1mesh and collect routinefixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
1MicroMesh loop

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
12.439.69880.2930.6197.213.5121952
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)
12.42.4689.70.910.6643.373.59

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 SYNTHESISTHROUGHOUT5ACH2.439.691253771396.360.190.18670.2476RANDOM21.366
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_deg31.51
r_dihedral_angle_4_deg12.539
r_dihedral_angle_3_deg10.473
r_dihedral_angle_1_deg7.173
r_angle_refined_deg1.464
r_angle_other_deg1.23
r_chiral_restr0.058
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.51
r_dihedral_angle_4_deg12.539
r_dihedral_angle_3_deg10.473
r_dihedral_angle_1_deg7.173
r_angle_refined_deg1.464
r_angle_other_deg1.23
r_chiral_restr0.058
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1788
Nucleic Acid Atoms
Solvent Atoms245
Heterogen Atoms15

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing