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Human beta-defensin-1 (Mutant Gln11Ala)
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 4.6 293 PEG 4000, AMMONIUM SULFATE, SODIUM ACETATE, GLYCEROL, pH 4.6, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.9 35.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.22 α = 90 b = 22.78 β = 108.5 c = 40.15 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 CCD MARMOSAIC 300 mm CCD 2005-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.97180 APS 22-BM
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 1.35 40 99.7 0.037 29 3.9 13193 13193 -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) 1.35 1.4 99.7 0.207 7.5 3.9 1284
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 1.35 30 13183 13183 926 99.72 0.154 0.154 0.151 0.1533 0.198 RANDOM 15.479
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] 0.61 -0.08 -0.29 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.191 r_dihedral_angle_4_deg 13.165 r_dihedral_angle_3_deg 12.562 r_dihedral_angle_1_deg 6.423 r_scangle_it 4.868 r_scbond_it 4.196 RIGID-BOND RESTRAINTS (A**2) 3.552 r_mcangle_it 2.744 r_mcbond_it 2.051 r_angle_refined_deg 1.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.191 r_dihedral_angle_4_deg 13.165 r_dihedral_angle_3_deg 12.562 r_dihedral_angle_1_deg 6.423 r_scangle_it 4.868 r_scbond_it 4.196 RIGID-BOND RESTRAINTS (A**2) 3.552 r_mcangle_it 2.744 r_mcbond_it 2.051 r_angle_refined_deg 1.862 r_nbtor_refined 0.306 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.212 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.139 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 SPHERICITY; FREE ATOMS (A**2) SPHERICITY; BONDED ATOMS (A**2)
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 541 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 19
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing