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Crystal structure of human alpha-defensin 6 (H27W mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZMQ PDB ENTRY 1ZMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 0.1 M imidazole, pH 6.5, 1M Na acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.88 34.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.774 α = 90 b = 32.675 β = 108.35 c = 54.005 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 IMAGE PLATE RIGAKU RAXIS IV++ 2009-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 1.949 50 99 0.105 0.088 16.5 5.7 8330 8258 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.949 1.98 92 0.579 0.504 2.5 4.7
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 1ZMQ 1.949 20 8330 7856 384 98.68 0.19487 0.19243 0.1938 0.24665 0.2487 RANDOM 37.237
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] 5.85 33.81 -14.83 8.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.097 r_dihedral_angle_3_deg 18.871 r_dihedral_angle_4_deg 13.844 r_dihedral_angle_1_deg 7.923 r_scangle_it 4.352 r_scbond_it 2.838 r_mcangle_it 1.839 r_angle_refined_deg 1.816 r_mcbond_it 0.998 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.097 r_dihedral_angle_3_deg 18.871 r_dihedral_angle_4_deg 13.844 r_dihedral_angle_1_deg 7.923 r_scangle_it 4.352 r_scbond_it 2.838 r_mcangle_it 1.839 r_angle_refined_deg 1.816 r_mcbond_it 0.998 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1036 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection SCALEPACK data scaling PHASER phasing