5R87

PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z44592329 in complex with INTERLEUKIN-1 BETA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.92912.8M ammonium sulphate, 0.1M Tris pH7.9
Crystal Properties
Matthews coefficientSolvent content
3.2261.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.65α = 90
b = 54.65β = 90
c = 75.05γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-23SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96871DiamondI24

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
11.4744.1899.60.050.0540.0210.99816.66.637383
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)
11.471.5199.81.6111.7470.6720.4686.62777

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 SYNTHESISTHROUGHOUT2NVH1.4744.2235465187799.560.19610.19530.2128RANDOM30.82
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]
-0.47-0.470.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.445
r_dihedral_angle_3_deg14.715
r_dihedral_angle_4_deg9.082
r_dihedral_angle_1_deg8.419
r_mcangle_it4.196
r_mcbond_other2.35
r_mcbond_it2.339
r_angle_refined_deg1.788
r_angle_other_deg1.368
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.445
r_dihedral_angle_3_deg14.715
r_dihedral_angle_4_deg9.082
r_dihedral_angle_1_deg8.419
r_mcangle_it4.196
r_mcbond_other2.35
r_mcbond_it2.339
r_angle_refined_deg1.788
r_angle_other_deg1.368
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1194
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing