2PBN

Crystal structure of the human tyrosine receptor phosphate gamma


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HY3PDB entry 2HY3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.5294100mM Sodium MES pH 6.5, 22% PEG 8000, 200mM Ammonium sulfate, VAPOR DIFFUSION, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.1260.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.338α = 90
b = 107.338β = 90
c = 67.757γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.10000NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.753.68399.80.0540.05416.110.2496774967731.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.71.79990.6450.6452.27.37108

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 entry 2HY31.7204961049610248599.830.2090.2080.234RANDOM41.844
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]
-0.63-0.31-0.630.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.267
r_dihedral_angle_4_deg16.741
r_dihedral_angle_3_deg13.437
r_dihedral_angle_1_deg5.466
r_scangle_it4.865
r_scbond_it3.075
r_mcangle_it1.948
r_angle_refined_deg1.527
r_mcbond_it1.283
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.267
r_dihedral_angle_4_deg16.741
r_dihedral_angle_3_deg13.437
r_dihedral_angle_1_deg5.466
r_scangle_it4.865
r_scbond_it3.075
r_mcangle_it1.948
r_angle_refined_deg1.527
r_mcbond_it1.283
r_nbtor_refined0.311
r_symmetry_vdw_refined0.266
r_nbd_refined0.202
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.126
r_chiral_restr0.115
r_bond_refined_d0.018
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2330
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms5

Software

Software
Software NamePurpose
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
CCP4data scaling