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Engineered human lipocalin 2 (C26) in complex with Y-DTPA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 293 2M dipotassium phosphate, 0.2M lithium sulfate, 0.1M CAPS/NaOH, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.97 58.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.26 α = 90 b = 113.26 β = 90 c = 119.98 γ = 90
Symmetry Space Group P 41 21 2
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 MARMOSAIC 225 mm CCD mirrors 2009-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 82.36 99.8 0.085 24.7 14.6 31147 31127 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 0.368 0.368 0.381 0.099 2.1 14.8 4470
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 (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 3DTQ 2.4 82.36 2 31127 31073 1567 99.76 0.2262 0.2238 0.2154 0.2696 0.2638 RANDOM 44.0647
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] 0.31 0.31 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.427 r_dihedral_angle_4_deg 21.535 r_dihedral_angle_3_deg 18.243 r_dihedral_angle_1_deg 6.888 r_scangle_it 3.889 r_scbond_it 2.322 r_mcangle_it 1.559 r_angle_refined_deg 1.514 r_mcbond_it 0.814 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.427 r_dihedral_angle_4_deg 21.535 r_dihedral_angle_3_deg 18.243 r_dihedral_angle_1_deg 6.888 r_scangle_it 3.889 r_scbond_it 2.322 r_mcangle_it 1.559 r_angle_refined_deg 1.514 r_mcbond_it 0.814 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4256 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 129
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection