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Crystal structure of the T27A mutant of human alpha defensin HNP4.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZMM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294 30% MPD
15% PEG 8000
100 mM sodium acetate pH 5.5
100 mM calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.12 41.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.704 α = 90 b = 38.989 β = 108.93 c = 71.13 γ = 90
Symmetry Space Group P 1 21 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 CCD MARMOSAIC 325 mm CCD 2016-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 0.97946 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.7 50 99.7 0.098 0.06 0.99 17.7 3.6 27445
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 99.9 0.66 0.67 1.2 3.6
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 1ZMM 1.7 33.73 26124 1383 99.9 0.27112 0.26909 0.2759 0.30998 0.3116 RANDOM 25.974
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] 1.88 -0.13 -2.76 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.43 r_dihedral_angle_4_deg 18.766 r_dihedral_angle_3_deg 15.751 r_dihedral_angle_1_deg 8.857 r_long_range_B_refined 4.737 r_long_range_B_other 4.71 r_scangle_other 2.076 r_angle_refined_deg 1.967 r_mcangle_it 1.889 r_mcangle_other 1.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.43 r_dihedral_angle_4_deg 18.766 r_dihedral_angle_3_deg 15.751 r_dihedral_angle_1_deg 8.857 r_long_range_B_refined 4.737 r_long_range_B_other 4.71 r_scangle_other 2.076 r_angle_refined_deg 1.967 r_mcangle_it 1.889 r_mcangle_other 1.888 r_scbond_other 1.449 r_scbond_it 1.448 r_mcbond_it 1.286 r_mcbond_other 1.285 r_angle_other_deg 0.973 r_chiral_restr 0.084 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 0.001 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 1940 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing