☰ Navigation Tabs
Human beta-defensin-1 (mutant Ser8Ala)
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 7 293 PEG 8000, LITHIUM SULFATE, pH 7.0, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.74 α = 73.9 b = 33.19 β = 85.5 c = 41.85 γ = 86.2
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 2005-08-10 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 30 92.6 0.051 29 6.4 14783 14783 -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) 1.65 1.71 85.8 0.207 6.4 5 1367
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 14783 14783 732 92.52 0.168 0.168 0.166 0.1653 0.204 RANDOM 17.276
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] -0.54 -0.03 -0.67 0.79 -0.3 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.18 r_dihedral_angle_4_deg 28.311 r_dihedral_angle_3_deg 13.365 r_dihedral_angle_1_deg 5.845 r_scangle_it 3.929 r_scbond_it 2.999 RIGID-BOND RESTRAINTS (A**2) 2.02 r_mcangle_it 1.926 r_angle_refined_deg 1.666 r_mcbond_it 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.18 r_dihedral_angle_4_deg 28.311 r_dihedral_angle_3_deg 13.365 r_dihedral_angle_1_deg 5.845 r_scangle_it 3.929 r_scbond_it 2.999 RIGID-BOND RESTRAINTS (A**2) 2.02 r_mcangle_it 1.926 r_angle_refined_deg 1.666 r_mcbond_it 1.35 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.27 r_nbd_refined 0.23 r_symmetry_hbond_refined 0.201 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 SPHERICITY; BONDED ATOMS (A**2)
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1092 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 34
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