7CHY

Crystal Structure Of Human Il-1beta In Complex With Antibody Binding Fragment Of IgG26


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I1B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.829317% (w/v) PEG 3350, 10% (v/v) glycerol, and 0.1 M citric acid at pH 3.8.
Crystal Properties
Matthews coefficientSolvent content
2.5451.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 156.344α = 90
b = 112.24β = 94.847
c = 38.577γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98CCDRAYONIX MX300-HS2015-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1.0NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.6519.7631000.7620.72.719167
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.740.76

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2I1B2.6519.71810396393.6960.2030.19980.253564.403
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]
2.4170.882-2.8150.245
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.821
r_dihedral_angle_3_deg14.438
r_dihedral_angle_4_deg13.349
r_dihedral_angle_1_deg7.079
r_lrange_it5.701
r_lrange_other5.594
r_mcangle_it2.606
r_mcangle_other2.606
r_scangle_it1.541
r_scangle_other1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.821
r_dihedral_angle_3_deg14.438
r_dihedral_angle_4_deg13.349
r_dihedral_angle_1_deg7.079
r_lrange_it5.701
r_lrange_other5.594
r_mcangle_it2.606
r_mcangle_other2.606
r_scangle_it1.541
r_scangle_other1.54
r_mcbond_it1.402
r_mcbond_other1.402
r_angle_refined_deg1.264
r_angle_other_deg1.106
r_scbond_it0.744
r_scbond_other0.744
r_nbd_other0.179
r_symmetry_nbd_other0.171
r_nbd_refined0.165
r_nbtor_refined0.156
r_xyhbond_nbd_refined0.14
r_symmetry_nbd_refined0.124
r_symmetry_xyhbond_nbd_refined0.098
r_symmetry_nbtor_other0.066
r_chiral_restr0.042
r_bond_refined_d0.004
r_bond_other_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4428
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing