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Structure of streptococcus pyogenes bacteriophage-associated hyaluronate lyase Hylp2
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 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.7 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.587 α = 90 b = 59.587 β = 90 c = 588.546 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 298 IMAGE PLATE MARRESEARCH MIRROR 2006-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5414
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 3.55 20 98.1 0.128 4.7 5360 5360
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 3.55 3.65 97.8 0.285 1.9
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2C3F 3.55 20 5360 4747 514 98.95 0.22273 0.22107 0.23625 RANDOM 48.47
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] 0.34 0.17 0.34 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.644 r_scangle_it 4.353 r_dihedral_angle_1_deg 3.101 r_scbond_it 2.307 r_mcangle_it 2.29 r_angle_refined_deg 1.773 r_mcbond_it 1.18 r_angle_other_deg 0.921 r_nbtor_other 0.297 r_symmetry_vdw_other 0.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.644 r_scangle_it 4.353 r_dihedral_angle_1_deg 3.101 r_scbond_it 2.307 r_mcangle_it 2.29 r_angle_refined_deg 1.773 r_mcbond_it 1.18 r_angle_other_deg 0.921 r_nbtor_other 0.297 r_symmetry_vdw_other 0.287 r_nbd_refined 0.254 r_nbd_other 0.242 r_symmetry_vdw_refined 0.207 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.102 r_xyhbond_nbd_other 0.066 r_symmetry_hbond_other 0.065 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2518 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing