☰ Navigation Tabs
Crystal structure of hyluranidase trimer at 2.6 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C3F PDB ENTRY 2C3F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 TRIS HCL, SODIUM FORMATE, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.67 53.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.801 α = 90 b = 58.801 β = 90 c = 586.102 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 203 CCD MARRESEARCH Mirror 2006-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 0.803 EMBL/DESY, HAMBURG X31
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 50 99.8 0.038 6.3 12713 12713
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 100 0.324 2.2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2C3F 2.6 50 12713 12090 623 99.57 0.19442 0.19304 0.1907 0.21913 RANDOM 48.041
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] 3.14 1.57 3.14 -4.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.95 r_dihedral_angle_4_deg 24.085 r_dihedral_angle_3_deg 18.27 r_scangle_it 8.051 r_dihedral_angle_1_deg 6.65 r_scbond_it 5.529 r_mcangle_it 3.682 r_mcbond_it 2.369 r_angle_refined_deg 1.635 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.95 r_dihedral_angle_4_deg 24.085 r_dihedral_angle_3_deg 18.27 r_scangle_it 8.051 r_dihedral_angle_1_deg 6.65 r_scbond_it 5.529 r_mcangle_it 3.682 r_mcbond_it 2.369 r_angle_refined_deg 1.635 r_nbtor_refined 0.326 r_nbd_refined 0.265 r_symmetry_vdw_refined 0.253 r_xyhbond_nbd_refined 0.176 r_symmetry_hbond_refined 0.168 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2515 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing