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Human beta-defensin-1 (Mutant Lys22Glu)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IJV PDB ENTRY 1IJV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 PEG 8000, AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.5, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.78 α = 73.6 b = 33.18 β = 85.3 c = 41.94 γ = 86.5
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 MAR scanner 345 mm plate Osmic mirrors 2005-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178
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 1.65 40 92.6 0.041 16 2.3 14844 14844 -3
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 1.65 1.71 87.1 0.156 5.3 2.2 1387
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 (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IJV 1.65 30 14844 14844 751 92.14 0.163 0.163 0.161 0.1712 0.195 RANDOM 20.81
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] -0.45 -0.29 -0.24 0.76 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.022 r_dihedral_angle_4_deg 28.853 r_dihedral_angle_3_deg 13.631 r_dihedral_angle_1_deg 5.972 r_scangle_it 3.706 r_scbond_it 2.742 r_angle_refined_deg 1.601 r_mcangle_it 1.539 r_mcbond_it 1.097 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.022 r_dihedral_angle_4_deg 28.853 r_dihedral_angle_3_deg 13.631 r_dihedral_angle_1_deg 5.972 r_scangle_it 3.706 r_scbond_it 2.742 r_angle_refined_deg 1.601 r_mcangle_it 1.539 r_mcbond_it 1.097 r_nbtor_refined 0.303 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.1 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 40
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing