☰ Navigation Tabs
Zebrafish TRAP1 bound to AMPPNP and calcium in the asymmetric closed state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IPE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 17% PEG-3350, 0.2 M sodium/potassium tartrate, 36 mM hexammine cobalt
Crystal Properties Matthews coefficient Solvent content 2.57 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.252 α = 90 b = 95.751 β = 134.66 c = 124.546 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 91.4 CCD ADSC QUANTUM 315r 2015-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115869 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.5 48.4 97.6 0.996 10.36 11.3 49472
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.693 97.39 0.453
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 4ipe 2.5 48.4 47254 2488 97.59 0.2312 0.2299 0.2323 0.2548 0.2534 RANDOM 70.791
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] 3.39 0.55 -1.82 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.698 r_dihedral_angle_4_deg 20.918 r_dihedral_angle_3_deg 20.399 r_dihedral_angle_1_deg 6.363 r_mcangle_it 4.161 r_angle_other_deg 3.562 r_mcbond_it 2.518 r_mcbond_other 2.518 r_angle_refined_deg 1.116 r_chiral_restr 0.286
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.698 r_dihedral_angle_4_deg 20.918 r_dihedral_angle_3_deg 20.399 r_dihedral_angle_1_deg 6.363 r_mcangle_it 4.161 r_angle_other_deg 3.562 r_mcbond_it 2.518 r_mcbond_other 2.518 r_angle_refined_deg 1.116 r_chiral_restr 0.286 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9531 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing