2QOD

Human EphA3 kinase and juxtamembrane region, Y602F mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GSFPDB entry 2GSF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529820 mg/mL Protein, 25% PEG 3350, 0.2M Ammonium sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8433.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.215α = 90
b = 38.289β = 102.43
c = 76.004γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.00000APS17-ID

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
11.154099.50.03613.23.9107783
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)
1.151.1999.70.6253.610706

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 2GSF1.1523.4107702541299.40.1930.1920.206RANDOM13.523
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.701
r_dihedral_angle_4_deg13.927
r_dihedral_angle_3_deg11.14
r_dihedral_angle_1_deg4.958
r_scangle_it1.947
r_scbond_it1.53
r_angle_refined_deg1.139
r_mcangle_it1.039
r_mcbond_it0.864
r_angle_other_deg0.819
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.701
r_dihedral_angle_4_deg13.927
r_dihedral_angle_3_deg11.14
r_dihedral_angle_1_deg4.958
r_scangle_it1.947
r_scbond_it1.53
r_angle_refined_deg1.139
r_mcangle_it1.039
r_mcbond_it0.864
r_angle_other_deg0.819
r_symmetry_vdw_refined0.212
r_nbd_refined0.207
r_nbd_other0.179
r_nbtor_refined0.176
r_symmetry_vdw_other0.174
r_mcbond_other0.138
r_symmetry_hbond_refined0.134
r_xyhbond_nbd_refined0.126
r_nbtor_other0.083
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2305
Nucleic Acid Atoms
Solvent Atoms370
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling