4G6M

Crystal structure of human IL-1beta in complex with therapeutic antibody binding fragment of gevokizumab


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PZ51PZ5, 3BKJ, 1TOO
experimental modelPDB 3BKJ1PZ5, 3BKJ, 1TOO
experimental modelPDB 1TOO1PZ5, 3BKJ, 1TOO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1529320% w/v PEG 4000, 0.2M ammonium formate supplemented with 10% w/v polyvinylpyrrolidone K15, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.884α = 90
b = 73.651β = 90
c = 111.254γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.8111.399.70.0850.09314.65.551619225.54
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.910014.65.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1PZ5, 3BKJ, 1TOO1.8126.55161950918258998.80.2030.2020.226RANDOM31.09
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]
-4.7131.55243.1607
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17.01
t_omega_torsion2.89
t_angle_deg1.02
t_bond_d0.007
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17.01
t_omega_torsion2.89
t_angle_deg1.02
t_bond_d0.007
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4501
Nucleic Acid Atoms
Solvent Atoms442
Heterogen Atoms

Software

Software
Software NamePurpose
XDSdata scaling
autoPROCdata collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
SCALAdata scaling