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Formation of a protein intermediate and its trapping by the simultaneous crystallization process: Crystal structure of an iron-saturated intermediate in the FE3+ binding pathway of camel lactoferrin at 2.7 resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DTZ PDB ENTRY 1DTZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 8 277 ethanol, pH 8.0, MICRODIALYSIS, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.64 53.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.91 α = 90 b = 80.62 β = 92.37 c = 56.29 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 288 IMAGE PLATE MARRESEARCH 2000-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.7 25 92 0.105 0.105 9.6 2.2 44276 19901 35.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.8 47 0.25 0.25 6.1 2.2 19901
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DTZ 2.7 25 0.01 44276 19901 961 94.1 0.22 0.188 0.188 0.255 RANDOM 57.1
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] -1.42 -0.9 0.49 0.93
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.3 c_angle_deg 2.7 c_improper_angle_d 1.78 c_bond_d 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5284 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement