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Glycosilated Human Serum Apo-tranferrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291.5 0.2 M Ammonium Citrate pH 7.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.99 58.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.631 α = 90 b = 102.148 β = 90 c = 199.969 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 PIXEL DECTRIS EIGER X 16M 2019-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.127 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3 37.35 99.9 0.096 0.104 0.038 0.999 9.9 7.3 36713
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 3 3.13 100 1.606 1.718 0.606 0.59 8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2HAV 3 37.35 1.34 36651 1829 99.89 0.221 0.2195 0.2494 0.2747 120.52
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.2261 f_angle_d 0.8525 f_chiral_restr 0.0448 f_plane_restr 0.0056 f_bond_d 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10488 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 117
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction MOLREP phasing