4QT8

Crystal Structure of RON Sema-PSI-IPT1 extracellular domains in complex with MSP beta-chain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.1 M Tris-HCl, pH 8.5, 20% w/v PEG4000, 8% v/v isopropanol, 4% v/v polypropylene glycol 400, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4950.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.585α = 90
b = 63.775β = 90.08
c = 146.049γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2010-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03320APS23-ID-B

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
12.996146.9691.80.2024.42.53967038960-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.996

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 4FWW & 2ASU319.983729935063188992.370.236770.233810.29077RANDOM51.191
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]
12.43-30.05-18.976.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.957
r_dihedral_angle_3_deg18.75
r_dihedral_angle_4_deg15.925
r_dihedral_angle_1_deg7.534
r_long_range_B_refined6.356
r_long_range_B_other6.355
r_mcangle_it5.942
r_mcangle_other3.815
r_mcbond_it3.47
r_mcbond_other3.466
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.957
r_dihedral_angle_3_deg18.75
r_dihedral_angle_4_deg15.925
r_dihedral_angle_1_deg7.534
r_long_range_B_refined6.356
r_long_range_B_other6.355
r_mcangle_it5.942
r_mcangle_other3.815
r_mcbond_it3.47
r_mcbond_other3.466
r_scangle_other2.842
r_scbond_it2.59
r_scbond_other1.664
r_angle_refined_deg1.391
r_angle_other_deg0.866
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12550
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms67

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling