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Crystal structure of the complex of hyaluranidase trimer with ascorbic acid at 3.1 A resolution reveals the locations of three binding sites
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C3F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 TRIS HCL, SODIUM FORMATE, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.68 54.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.502 α = 90 b = 58.502 β = 90 c = 583.54 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 2007-03-10 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 3.1 50 90 0.11 11.7 6874 6874
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) 3.1 3.15 92 0.434 2.67
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2C3F 3.1 50 6874 6358 516 90 0.212 0.204 0.197 0.1985 0.234 0.2833 RANDOM 51.59
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] 4.68 2.34 4.68 -7.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.545 r_dihedral_angle_4_deg 25.745 r_dihedral_angle_3_deg 20.869 r_dihedral_angle_1_deg 8.095 r_scangle_it 4.489 r_scbond_it 3.137 r_angle_refined_deg 2.311 r_mcangle_it 2.125 r_mcbond_it 1.672 r_nbtor_refined 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.545 r_dihedral_angle_4_deg 25.745 r_dihedral_angle_3_deg 20.869 r_dihedral_angle_1_deg 8.095 r_scangle_it 4.489 r_scbond_it 3.137 r_angle_refined_deg 2.311 r_mcangle_it 2.125 r_mcbond_it 1.672 r_nbtor_refined 0.332 r_nbd_refined 0.308 r_symmetry_vdw_refined 0.3 r_symmetry_hbond_refined 0.227 r_xyhbond_nbd_refined 0.225 r_chiral_restr 0.12 r_bond_refined_d 0.023 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2515 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement SCALEPACK data scaling