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Crystal structure of human alpha-defensin 5, HD5 (Thr7Arg Glu21Arg mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZMP PDB entry 1ZMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294.15 0.1M MES pH 6.5, 0.5M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K
Crystal Properties Matthews coefficient Solvent content 1.82 32.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 20.55 α = 90 b = 51.703 β = 96.35 c = 50.676 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 PIXEL PSI PILATUS 6M 2014-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979 SSRL BL12-2
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 1.5 36.08 90.5 0.089 28.6 3.1 16958 15346
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.8 93.1 0.623 2.8 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB entry 1ZMP 1.5 36.077 16081 14565 766 90.46 0.1841 0.18205 0.1898 0.22131 0.2299 RANDOM 25.384
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] -0.35 0.1 1 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 19.413 r_dihedral_angle_3_deg 13.945 r_dihedral_angle_2_deg 11.691 r_dihedral_angle_1_deg 7.541 r_mcangle_it 3.221 r_scbond_it 3.002 r_mcbond_it 2.197 r_mcbond_other 2.191 r_angle_refined_deg 2.07 r_angle_other_deg 0.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 19.413 r_dihedral_angle_3_deg 13.945 r_dihedral_angle_2_deg 11.691 r_dihedral_angle_1_deg 7.541 r_mcangle_it 3.221 r_scbond_it 3.002 r_mcbond_it 2.197 r_mcbond_other 2.191 r_angle_refined_deg 2.07 r_angle_other_deg 0.871 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1000 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 47
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling