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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 1.93 36.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.84 α = 90 b = 23.57 β = 107 c = 40.45 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 MAR scanner 345 mm plate Osmic mirrors 2005-07-21 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 1.49 50 92.8 0.055 26 5.1 9213 9213 -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) 1.49 1.54 77.2 0.266 4.5 3.5 741
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 1.49 30 9202 9202 652 93.17 0.138 0.138 0.134 0.1331 0.199 RANDOM 14.28
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] -0.19 -0.63 -0.05 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.945 r_dihedral_angle_4_deg 22.935 r_dihedral_angle_3_deg 9.715 r_dihedral_angle_1_deg 5.983 r_scangle_it 3.14 r_mcangle_it 2.782 r_scbond_it 2.279 r_mcbond_it 2.179 RIGID-BOND RESTRAINTS (A**2) 1.829 r_angle_refined_deg 1.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.945 r_dihedral_angle_4_deg 22.935 r_dihedral_angle_3_deg 9.715 r_dihedral_angle_1_deg 5.983 r_scangle_it 3.14 r_mcangle_it 2.782 r_scbond_it 2.279 r_mcbond_it 2.179 RIGID-BOND RESTRAINTS (A**2) 1.829 r_angle_refined_deg 1.569 r_nbtor_refined 0.321 r_nbd_refined 0.283 r_symmetry_hbond_refined 0.21 r_xyhbond_nbd_refined 0.198 r_symmetry_vdw_refined 0.177 r_chiral_restr 0.147 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 SPHERICITY; FREE ATOMS (A**2) SPHERICITY; BONDED ATOMS (A**2)
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 538 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 14
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