2V5Y

Crystal structure of the receptor protein tyrosine phosphatase mu ectodomain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C9APDB ENTRY 2C9A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17100MM BIS-TRIS-PROPANE, PH 6.5 22.5% (W/V) PEG-SMEAR, 200MM K-THIOCYANATE
Crystal Properties
Matthews coefficientSolvent content
3.0760

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.336α = 90
b = 69.325β = 113.52
c = 97.487γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
13.12098.60.1610.35.319030
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)
13.13.2890.612.54.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 2C9A3.120177929691000.2460.2420.32RANDOM27.1
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]
-5.03-1.945.12-1.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.455
r_dihedral_angle_3_deg19.584
r_dihedral_angle_4_deg16.173
r_dihedral_angle_1_deg7.602
r_angle_refined_deg1.243
r_mcangle_it0.858
r_angle_other_deg0.836
r_scangle_it0.752
r_mcbond_it0.481
r_scbond_it0.378
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.455
r_dihedral_angle_3_deg19.584
r_dihedral_angle_4_deg16.173
r_dihedral_angle_1_deg7.602
r_angle_refined_deg1.243
r_mcangle_it0.858
r_angle_other_deg0.836
r_scangle_it0.752
r_mcbond_it0.481
r_scbond_it0.378
r_symmetry_vdw_other0.223
r_nbd_refined0.187
r_nbd_other0.187
r_nbtor_refined0.181
r_symmetry_vdw_refined0.175
r_xyhbond_nbd_refined0.154
r_symmetry_hbond_refined0.134
r_nbtor_other0.087
r_chiral_restr0.074
r_mcbond_other0.041
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4423
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms100

Software

Software
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PHASERphasing
REFMACrefinement