☰ Navigation Tabs
Structure of D128N streptavidin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.05 M HEPES, pH 7.5 with 7.5% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.597 α = 90 b = 98.95 β = 112.58 c = 52.638 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 PIXEL PSI PILATUS 6M 2011-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.0 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.351 34.672 97 0.042 0.048 0.022 16.6 4.5 101243 101243
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.42 93.9 1.096 1.096 0.564 0.7 4.5 14280
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1MEP 1.351 33.97 101213 96132 5081 96.97 0.1289 0.1268 0.133 0.1702 0.1734 RANDOM 16.922
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] 0.05 -0.03 -0.64 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.902 r_dihedral_angle_4_deg 15.639 r_dihedral_angle_3_deg 11.482 r_sphericity_free 10.829 r_sphericity_bonded 6.837 r_dihedral_angle_1_deg 6.801 r_scangle_it 5.87 r_mcangle_it 4.638 r_scbond_it 4.606 r_mcbond_it 3.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.902 r_dihedral_angle_4_deg 15.639 r_dihedral_angle_3_deg 11.482 r_sphericity_free 10.829 r_sphericity_bonded 6.837 r_dihedral_angle_1_deg 6.801 r_scangle_it 5.87 r_mcangle_it 4.638 r_scbond_it 4.606 r_mcbond_it 3.611 r_mcbond_other 3.326 r_rigid_bond_restr 2.419 r_angle_refined_deg 1.77 r_angle_other_deg 0.991 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3569 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 64
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction