☰ Navigation Tabs
Human raf kinase inhibitor protein (rkip) in complex with o-phosphotyrosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BEH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 Initial 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 coefficient Solvent content 1.99 38.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.674 α = 90 b = 33.892 β = 96.09 c = 59.705 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD BRUKER SMART 6000 2003-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE MACSCIENCE 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.948 59.76 95.4 0.081 18.2 5.7 12443 11833 2 2 19.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.948 2.02 78.7 0.234 3.7 3.4 951
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1BEH 1.948 59.76 11832 572 95.1 0.157 0.154 0.165 0.208 0.2197 RANDOM 19.68
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] 1.5 0.98 0.62 -1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.07 r_scangle_it 3.821 r_scbond_it 2.512 r_angle_refined_deg 1.649 r_mcangle_it 1.598 r_mcbond_it 0.94 r_angle_other_deg 0.914 r_symmetry_vdw_other 0.312 r_nbd_other 0.246 r_symmetry_vdw_refined 0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.07 r_scangle_it 3.821 r_scbond_it 2.512 r_angle_refined_deg 1.649 r_mcangle_it 1.598 r_mcbond_it 0.94 r_angle_other_deg 0.914 r_symmetry_vdw_other 0.312 r_nbd_other 0.246 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.107 r_nbtor_other 0.085 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1473 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 17
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection HKL-2000 data reduction HKL-2000 data scaling