2QYQ

Human raf kinase inhibitor protein (rkip) in complex with o-phosphotyrosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BEH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7291Initial crystallisation: 32-34% PEG 4OOO or 8000, 0.2 M sodium acetate, 0.1 M sodium acetate pH 4.0. Complex formed by soaking in: 32% PEG 4OOO, 0.2 M sodium chloride, 0.1 M O-phosphotyrosine, 0.1 M hepes pH 7.0., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9938.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.674α = 90
b = 33.892β = 96.09
c = 59.705γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002003-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEMACSCIENCE1.5418

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
11.94859.7695.40.08118.25.712443118332219.68
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)
1.9482.0278.70.2343.73.4951

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 REPLACEMENTTHROUGHOUT1BEH1.94859.761183257295.10.1570.1540.208RANDOM19.68
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]
1.50.980.62-1.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.07
r_scangle_it3.821
r_scbond_it2.512
r_angle_refined_deg1.649
r_mcangle_it1.598
r_mcbond_it0.94
r_angle_other_deg0.914
r_symmetry_vdw_other0.312
r_nbd_other0.246
r_symmetry_vdw_refined0.207
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.07
r_scangle_it3.821
r_scbond_it2.512
r_angle_refined_deg1.649
r_mcangle_it1.598
r_mcbond_it0.94
r_angle_other_deg0.914
r_symmetry_vdw_other0.312
r_nbd_other0.246
r_symmetry_vdw_refined0.207
r_nbd_refined0.202
r_symmetry_hbond_refined0.168
r_xyhbond_nbd_refined0.156
r_chiral_restr0.107
r_nbtor_other0.085
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1473
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms17

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
HKL-2000data reduction
HKL-2000data scaling