5R8A

PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z1492796719 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
3.2261.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.6α = 90
b = 54.6β = 90
c = 75.26γ = 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
11.4754.61000.0460.050.0190.99917.86.637554
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)
11.471.5199.91.4941.6230.6290.5096.52774

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 SYNTHESISTHROUGHOUT2NVH1.4754.635631188599.970.19330.19190.2197RANDOM28.057
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]
-0.31-0.310.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.828
r_dihedral_angle_3_deg13.777
r_dihedral_angle_4_deg10.099
r_dihedral_angle_1_deg7.934
r_mcangle_it4.06
r_mcbond_other2.525
r_mcbond_it2.511
r_angle_refined_deg1.786
r_angle_other_deg1.378
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.828
r_dihedral_angle_3_deg13.777
r_dihedral_angle_4_deg10.099
r_dihedral_angle_1_deg7.934
r_mcangle_it4.06
r_mcbond_other2.525
r_mcbond_it2.511
r_angle_refined_deg1.786
r_angle_other_deg1.378
r_chiral_restr0.093
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1190
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing