5R8J

PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z355728146 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
3.2361.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.6α = 90
b = 54.6β = 90
c = 75.3γ = 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
11.6244.21000.0790.0850.0330.99813.16.628133
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)
11.621.661001.8712.0310.7850.3996.62096

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 SYNTHESISTHROUGHOUT2NVH1.6244.2426713138699.930.19050.18930.2138RANDOM29.932
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]
-0.35-0.350.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.138
r_dihedral_angle_3_deg15.249
r_dihedral_angle_4_deg12.624
r_dihedral_angle_1_deg7.873
r_mcangle_it4.12
r_mcbond_other2.327
r_mcbond_it2.311
r_angle_refined_deg1.63
r_angle_other_deg1.343
r_chiral_restr0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.138
r_dihedral_angle_3_deg15.249
r_dihedral_angle_4_deg12.624
r_dihedral_angle_1_deg7.873
r_mcangle_it4.12
r_mcbond_other2.327
r_mcbond_it2.311
r_angle_refined_deg1.63
r_angle_other_deg1.343
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1190
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing