4DKD

Crystal Structure of Human Interleukin-34 Bound to Human CSF-1R


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.1M Calcium acetate, 0.1M Mes pH 6.0, 15% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.4764.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.361α = 90
b = 101.361β = 90
c = 175.252γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0000ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
135099.80.06123.57.621502
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.1199.80.6272.87

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT35020213109098.990.253960.252270.28677RANDOM97.365
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]
1.040.521.04-1.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.4
r_dihedral_angle_3_deg15.606
r_dihedral_angle_4_deg15.421
r_dihedral_angle_1_deg5.459
r_mcangle_it1.141
r_scangle_it1.137
r_angle_refined_deg0.991
r_mcbond_it0.632
r_scbond_it0.604
r_chiral_restr0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.4
r_dihedral_angle_3_deg15.606
r_dihedral_angle_4_deg15.421
r_dihedral_angle_1_deg5.459
r_mcangle_it1.141
r_scangle_it1.137
r_angle_refined_deg0.991
r_mcbond_it0.632
r_scbond_it0.604
r_chiral_restr0.06
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4722
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms134

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling