☰ Navigation Tabs
Arg-modified human beta-defensin 1 (HBD1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model ModelArchive ma-chlmo entry 2IJV that was moved from PDB to ModelArchive
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.0 M Lithium sulfate, 2% (w/v) PEG8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.9 35.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 20.366 α = 90 b = 27.408 β = 90 c = 55.079 γ = 90
Symmetry Space Group P 21 21 21
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 mirrors 2007-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.96 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.36 30 99.6 0.087 0.087 17 5.7 7002 7002 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.36 1.41 99.4 0.341 0.341 4.2 5.2 657
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 2IJV 1.36 20 7002 6636 332 99.64 0.10776 0.10776 0.10528 0.1091 0.15797 RANDOM 12.36
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] -0.68 0.66 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.896 r_dihedral_angle_4_deg 20.509 r_sphericity_free 9.528 r_dihedral_angle_3_deg 8.497 r_scangle_it 5.911 r_dihedral_angle_1_deg 5.639 r_sphericity_bonded 5.324 r_scbond_it 4.253 r_mcangle_it 3.076 r_mcbond_it 2.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.896 r_dihedral_angle_4_deg 20.509 r_sphericity_free 9.528 r_dihedral_angle_3_deg 8.497 r_scangle_it 5.911 r_dihedral_angle_1_deg 5.639 r_sphericity_bonded 5.324 r_scbond_it 4.253 r_mcangle_it 3.076 r_mcbond_it 2.402 r_rigid_bond_restr 2.359 r_angle_refined_deg 1.963 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.214 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.194 r_symmetry_vdw_refined 0.192 r_chiral_restr 0.113 r_bond_refined_d 0.02 r_gen_planes_refined 0.017 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 279 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing