X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Details THE COMPLEX OF THE IL-1 RECEPTOR WITH THE ANTAGONIST WAS PREPARED BY MIXING A SOLUTION OF IL-1 RECEPTOR IN 50 MM TRIS (PH 7.5) AND 150 MM NACL WITH A SOLUTION OF IL1RA IN THE SAME BUFFER. THE COMPLEX WAS CRYSTALLIZED USING THE HANGING DROP METHOD. THE DROPS WERE PREPARED BY MIXING 4 UL OF THE PROTEIN SOLUTION WITH 1 UL OF RESERVOIR SOLUTION, CONTAINING 30% (W/V) PEG 3350, 400 MM MGCL2 IN 100 MM MOPS BUFFER (PH 7.0)., vapor diffusion - hanging drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.2 α = 90
b = 84.6 β = 90
c = 140.2 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 296
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR SIEMENS COLLIMATOR 1994-09
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE MACSCIENCE M18XH -- -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.7 60 97.2 -- 0.06 -- 4.7 -- 15631 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.7 2.8 85.3 -- 0.325 -- 3.1 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MIR + MOLECULAR REPLACEMENT 2.7 8.0 -- -- -- 15012 -- 97.6 -- 0.213 0.213 0.314 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.7 2.82 -- 172 1463 0.393 0.466 -- 86.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 45.2
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 17.7
x_scbond_it 8.3
x_mcangle_it 11.5
x_mcbond_it 5.4
x_improper_angle_d 1.0
x_bond_d 0.004
x_angle_deg 1.2
x_dihedral_angle_d 26.5
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3638
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 86

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SQUASH, X-PLOR3.1 Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
X-PLOR version: 3.1 model building
SQUASH model building
XSCALE data reduction
XDS data collection