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Engineered lipocalin C3A5 in complex with a transition state analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N47
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 PEG 3350, ammonium tartrate
Crystal Properties Matthews coefficient Solvent content 2.4 48.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.385 α = 90 b = 39.034 β = 120 c = 96.385 γ = 90
Symmetry Space Group P 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 100 PIXEL DECTRIS PILATUS3 2M Si-mirror 2018-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91840 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.294 83.472 95.3 0.256 0.1 4.9 6.2 55375
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 1.8 1.9 95.2 0.39 0.39 0.431 0.178 1.4 5.7
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 5N47 1.8 41.74 52693 2681 94.83 0.1622 0.1608 0.1664 0.1899 0.1943 RANDOM 19.936
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] -2.47 -4.5 3.91 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.579 r_dihedral_angle_4_deg 19.657 r_dihedral_angle_3_deg 16.721 r_dihedral_angle_1_deg 7.599 r_angle_refined_deg 1.633 r_angle_other_deg 1.137 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.579 r_dihedral_angle_4_deg 19.657 r_dihedral_angle_3_deg 16.721 r_dihedral_angle_1_deg 7.599 r_angle_refined_deg 1.633 r_angle_other_deg 1.137 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4334 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 78
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction