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Crystal Structure of a Domain-Opened Mutant (R121D) of the Human Lactoferrin N-lobe Refined From a Merohedrally-Twinned Crystal Form.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LCT pdb entry 1lct
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 8 298 concentrated solution of the protein (50-80 mg mL-1), 0.01 M Tris-HCl, pH 8.0, 12% (v/v) isopropanol, MICRODIALYSIS, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.35 71.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.3 α = 90 b = 151.3 β = 90 c = 48.6 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 IMAGE PLATE RIGAKU RAXIS IIC graphite monochromator 1994-03-01 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) 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 50 96 0.115 6.1 2.8 23431 4
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) 3 3.11 93 0.418 0.418 1.8 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 pdb entry 1lct 3 10 2 4 23431 21955 795 93.9 0.1413 0.139 0.13 0.199 0.1759 RANDOM,
PLUS TWIN-RELATED MATES 31.1
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 5241
RMS Deviations Key Refinement Restraint Deviation s_from_restr_planes 0.177 s_non_zero_chiral_vol 0.03 s_similar_adp_cmpnt 0.026 s_zero_chiral_vol 0.023 s_angle_d 0.017 s_anti_bump_dis_restr 0.017 s_similar_dist 0.012 s_bond_d 0.005 s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5114 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction ROTAVATA data reduction X-PLOR model building BRUTE model building SHELXL-97 refinement CCP4 data scaling ROTAVATA data scaling X-PLOR phasing BRUTE phasing