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Crystal structure of a putative peptide-binding domain of MpAFP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SAD model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.6 296 Calcium chloride, sodium acetate, PEG400
Crystal Properties Matthews coefficient Solvent content 2.87 57.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.115 α = 66.25 b = 61.065 β = 72.66 c = 63.473 γ = 67.94
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD RAYONIX MX300HE 2016-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 47.64 98 0.207 0.163 6.4 4.4 41606
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 96.8 1.79 0.368 0.9 4.4
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 SAD model 2 47.64 39645 1960 98.01 0.1851 0.18328 0.1887 0.22143 0.2256 RANDOM 42.369
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] -0.39 -0.57 0.88 0.77 -2.02 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.774 r_dihedral_angle_3_deg 15.972 r_dihedral_angle_4_deg 15.367 r_long_range_B_refined 9.454 r_long_range_B_other 9.441 r_scangle_other 7.684 r_dihedral_angle_1_deg 6.733 r_scbond_it 5.063 r_scbond_other 5.056 r_mcangle_it 4.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.774 r_dihedral_angle_3_deg 15.972 r_dihedral_angle_4_deg 15.367 r_long_range_B_refined 9.454 r_long_range_B_other 9.441 r_scangle_other 7.684 r_dihedral_angle_1_deg 6.733 r_scbond_it 5.063 r_scbond_other 5.056 r_mcangle_it 4.702 r_mcangle_other 4.701 r_mcbond_it 3.277 r_mcbond_other 3.276 r_angle_refined_deg 1.721 r_angle_other_deg 1.038 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3761 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing