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Crystal structure of the G23A 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% isopropanol
10% PEG 1500
200 mM lithium sulfate
100 mM sodium acetate pH 5.5
Crystal Properties Matthews coefficient Solvent content 1.9 35.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.629 α = 90 b = 65.894 β = 90 c = 124.064 γ = 90
Symmetry Space Group P 21 21 21
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 1.67 50 99.8 0.057 0.031 0.99 28.8 4.2 40384
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 99.9 0.966 0.521 0.71 4.2 1991
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1ZMM 1.67 34.567 0.5 40053 2011 98.89 0.2198 0.218 0.22 0.2531 0.2528
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.779 f_angle_d 1.32 f_chiral_restr 0.062 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2964 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 126
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing