1XK4

Crystal structure of human calprotectin(S100A8/S100A9)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.228532% MPD, 0.1M Citrate (pH= 4.2), 20mM Tris (pH= 8.0), 2mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.447.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.509α = 90
b = 78.697β = 94.94
c = 177.411γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-11-15MSINGLE WAVELENGTH
21100IMAGE PLATEMARRESEARCH2004-07-28
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.97960SLSX06SA
2SYNCHROTRONBESSY BEAMLINE 14.20.92000BESSY14.2

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
11.83081.030.1193.80056.21026359950766
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)
11.81.969.880.481.446.112460

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT1MR8 and 1IRJ1.830-39980294798500481.020.16020.157810.20475RANDOM27.208
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]
2.25-1.05-1.59-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.494
r_dihedral_angle_3_deg16.05
r_dihedral_angle_4_deg14.033
r_dihedral_angle_1_deg5.481
r_scangle_it3.808
r_mcangle_it2.93
r_scbond_it2.494
r_mcbond_it2.05
r_angle_refined_deg1.458
r_symmetry_vdw_refined0.372
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.494
r_dihedral_angle_3_deg16.05
r_dihedral_angle_4_deg14.033
r_dihedral_angle_1_deg5.481
r_scangle_it3.808
r_mcangle_it2.93
r_scbond_it2.494
r_mcbond_it2.05
r_angle_refined_deg1.458
r_symmetry_vdw_refined0.372
r_nbtor_refined0.315
r_xyhbond_nbd_refined0.255
r_symmetry_hbond_refined0.254
r_nbd_refined0.225
r_metal_ion_refined0.118
r_chiral_restr0.115
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8880
Nucleic Acid Atoms
Solvent Atoms1059
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing