2NVH

Determination of Solvent Content in Cavities in Interleukin-1 Using Experimentally-Phased Electron Density


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5I1BPDB ENTRY 5I1B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5298Well solution of 2.2 - 2.8 M ammonium sulfate, 100 mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
3.2261.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.506α = 90
b = 54.506β = 90
c = 75.359γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 41999-07-10MSINGLE WAVELENGTH
21
31
41
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.527.299.90.04649.13525919.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.551000.2988.1

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 (All)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNONEPDB ENTRY 5I1B1.5327.235287352251000.2110.211
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]
RMS Deviations
KeyRefinement Restraint Deviation
t_dihedral_angle_d18.684
t_it14.285
t_angle_deg2.946
t_nbd0.039
t_bond_d0.025
t_gen_planes0.021
t_trig_c_planes0.012
t_incorr_chiral_ct
t_pseud_angle
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1224
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms10

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
TNTrefinement
PDB_EXTRACTdata extraction
EPMRphasing