3EKA

Crystal structure of the complex of hyaluranidase trimer with ascorbic acid at 3.1 A resolution reveals the locations of three binding sites


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C3F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8298TRIS HCL, SODIUM FORMATE, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6854.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.502α = 90
b = 58.502β = 90
c = 583.54γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray203CCDMARRESEARCHMIRROR2007-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X310.803EMBL/DESY, HAMBURGX31

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.150900.1111.768746874
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.13.15920.4342.67

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2C3F3.15068746358516900.2120.2040.1970.234RANDOM51.59
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]
4.682.344.68-7.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.545
r_dihedral_angle_4_deg25.745
r_dihedral_angle_3_deg20.869
r_dihedral_angle_1_deg8.095
r_scangle_it4.489
r_scbond_it3.137
r_angle_refined_deg2.311
r_mcangle_it2.125
r_mcbond_it1.672
r_nbtor_refined0.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.545
r_dihedral_angle_4_deg25.745
r_dihedral_angle_3_deg20.869
r_dihedral_angle_1_deg8.095
r_scangle_it4.489
r_scbond_it3.137
r_angle_refined_deg2.311
r_mcangle_it2.125
r_mcbond_it1.672
r_nbtor_refined0.332
r_nbd_refined0.308
r_symmetry_vdw_refined0.3
r_symmetry_hbond_refined0.227
r_xyhbond_nbd_refined0.225
r_chiral_restr0.12
r_bond_refined_d0.023
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2515
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms36

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling