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Crystal structure of Human Defensin-5 Y27A mutant crystal form 2.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 3 M sodium chloride, 5% MPD, 0.1 M calcium chloride, and 0.1 M imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.758 α = 90 b = 59.758 β = 105.54 c = 47.284 γ = 90
Symmetry Space Group C 1 2 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 Rh coated mirror 2015-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 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 2.08 50 97.4 0.109 11 3.3 11584 11584
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 2.08 2.13 92.3 0.538 1.1 2.6
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 1ZMP 2.08 45.74 10420 582 97.12 0.23729 0.23454 0.2382 0.29206 0.2949 RANDOM 54.198
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] -1.29 2.11 -0.54 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.395 r_dihedral_angle_4_deg 10.827 r_dihedral_angle_2_deg 9.914 r_dihedral_angle_1_deg 5.972 r_long_range_B_refined 2.901 r_long_range_B_other 2.67 r_angle_refined_deg 1.109 r_angle_other_deg 0.806 r_mcangle_it 0.61 r_mcangle_other 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.395 r_dihedral_angle_4_deg 10.827 r_dihedral_angle_2_deg 9.914 r_dihedral_angle_1_deg 5.972 r_long_range_B_refined 2.901 r_long_range_B_other 2.67 r_angle_refined_deg 1.109 r_angle_other_deg 0.806 r_mcangle_it 0.61 r_mcangle_other 0.61 r_scangle_other 0.586 r_mcbond_it 0.352 r_mcbond_other 0.352 r_scbond_it 0.346 r_scbond_other 0.346 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 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 1428 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing