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Crystal structure of human translationally controlled tumour associated protein (hTCTP) mutant E12V
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YZ1 PDB ENTRY 1YZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 277 0.1M Tris, pH 8.2, 22% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.7 54.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.192 α = 90 b = 81.543 β = 90 c = 139.92 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 210 2008-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.6 50 97.5 0.096 0.096 13.6 4 28188 27483
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) Redundancy Number Unique Reflections (All) 2.6 2.69 97.5 0.467 0.467 2.9 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1YZ1 2.6 36 26812 26115 1366 97.4 0.23883 0.23883 0.23657 0.2355 0.28031 0.246 RANDOM 55.88
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] -2.24 7.4 -5.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.026 r_dihedral_angle_4_deg 18.239 r_dihedral_angle_3_deg 15.131 r_scangle_it 6.503 r_dihedral_angle_1_deg 4.505 r_mcangle_it 4.263 r_scbond_it 4.078 r_rigid_bond_restr 3.453 r_mcbond_it 3.118 r_sphericity_free 1.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.026 r_dihedral_angle_4_deg 18.239 r_dihedral_angle_3_deg 15.131 r_scangle_it 6.503 r_dihedral_angle_1_deg 4.505 r_mcangle_it 4.263 r_scbond_it 4.078 r_rigid_bond_restr 3.453 r_mcbond_it 3.118 r_sphericity_free 1.227 r_sphericity_bonded 1.004 r_angle_refined_deg 0.897 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4788 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling