7CHZ

Crystal Structure Of Human Il-1beta In Complex With Antibody Binding Fragment Of IgG26A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429317% (w/v) PEG 3350, 10% (v/v) glycerol, and 0.1 M citric acid at pH 4.0
Crystal Properties
Matthews coefficientSolvent content
2.652.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.694α = 90
b = 112.699β = 94.531
c = 38.935γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98CCDRAYONIX MX-2252016-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
12.482598.90.8828.83.723536
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)
12.482.570.88

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-VALUE2I1B2.523.94122991114298.9160.1960.19260.259552.161
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]
0.1110.3840.164-0.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.57
r_dihedral_angle_4_deg19.719
r_dihedral_angle_3_deg16.187
r_dihedral_angle_1_deg8.14
r_lrange_it6.81
r_lrange_other6.759
r_mcangle_it3.958
r_mcangle_other3.957
r_scangle_it3.006
r_scangle_other3.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.57
r_dihedral_angle_4_deg19.719
r_dihedral_angle_3_deg16.187
r_dihedral_angle_1_deg8.14
r_lrange_it6.81
r_lrange_other6.759
r_mcangle_it3.958
r_mcangle_other3.957
r_scangle_it3.006
r_scangle_other3.006
r_mcbond_it2.223
r_mcbond_other2.221
r_scbond_it1.643
r_scbond_other1.641
r_angle_refined_deg1.58
r_angle_other_deg1.215
r_symmetry_nbd_refined0.237
r_nbd_other0.22
r_symmetry_nbd_other0.186
r_nbd_refined0.18
r_xyhbond_nbd_refined0.177
r_nbtor_refined0.164
r_symmetry_xyhbond_nbd_refined0.132
r_symmetry_nbtor_other0.083
r_chiral_restr0.066
r_symmetry_xyhbond_nbd_other0.033
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4465
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms

Software

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