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Human serum trnasferrin bound to a fluorescent probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X1B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 298 PIPES-Na 0.1M pH 6.6, disodium malonate 8mM, PEG 3350 17%, glycerol 18%
Crystal Properties Matthews coefficient Solvent content 3.84 67.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.012 α = 90 b = 155.752 β = 90 c = 107.554 γ = 90
Symmetry Space Group C 2 2 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 315r 2014-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.93001 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.85 103.29 99.7 0.078 0.084 0.029 9.8 8 27148
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.95 100 0.794 0.848 0.296 0.905 8.1
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 4X1B 2.86 103.29 25317 1283 97.48 0.1576 0.1537 0.1593 0.2352 0.2327 RANDOM 63.835
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] -3.82 1.84 1.98
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 62.931 r_dihedral_angle_2_deg 35.643 r_dihedral_angle_3_deg 17.343 r_dihedral_angle_4_deg 15.959 r_dihedral_angle_1_deg 5.951 r_rigid_bond_restr 3.851 r_angle_refined_deg 1.381 r_angle_other_deg 1.019 r_chiral_restr 0.078 r_bond_refined_d 0.013
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 62.931 r_dihedral_angle_2_deg 35.643 r_dihedral_angle_3_deg 17.343 r_dihedral_angle_4_deg 15.959 r_dihedral_angle_1_deg 5.951 r_rigid_bond_restr 3.851 r_angle_refined_deg 1.381 r_angle_other_deg 1.019 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4997 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 77
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER model building