☰ Navigation Tabs
Crystal Structure of E.coli transthyretin-related protein with bound Zn and Br
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 25% PEG 550 MME, 100mM MES, 10mM ZnSO4 (Crystal soaked in crystallization buffer enriched with 100mM NaBr for 12h prior to data collection), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.21 44.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.72 α = 90 b = 92.03 β = 103.5 c = 57.49 γ = 90
Symmetry Space Group P 1 21 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 MARRESEARCH 2001-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8033 EMBL/DESY, HAMBURG X13
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 2.1 20 96.3 0.047 27.1 25512 25512
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 2.1 2.3 93.6 0.2 10
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 1F41 2.1 17.38 24310 24310 1300 97.51 0.17752 0.17752 0.17482 0.185 0.22903 0.2336 RANDOM 19.438
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] 0.04 0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.731 r_scangle_it 2.583 r_scbond_it 1.759 r_angle_refined_deg 1.334 r_mcangle_it 0.941 r_angle_other_deg 0.768 r_mcbond_it 0.516 r_symmetry_vdw_refined 0.283 r_symmetry_vdw_other 0.272 r_nbd_other 0.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.731 r_scangle_it 2.583 r_scbond_it 1.759 r_angle_refined_deg 1.334 r_mcangle_it 0.941 r_angle_other_deg 0.768 r_mcbond_it 0.516 r_symmetry_vdw_refined 0.283 r_symmetry_vdw_other 0.272 r_nbd_other 0.244 r_nbd_refined 0.187 r_symmetry_hbond_refined 0.187 r_metal_ion_refined 0.178 r_xyhbond_nbd_refined 0.155 r_nbtor_other 0.086 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3618 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling