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Crystal structure of Streptococcus Pneumoniae Hyaluronate Lyase from 30percent PEGMME.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EGU PDB ENTRY 1EGU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 30% POLYETHYLENE GLYCOL MONOMETHYL ETHER (PEGMME) 2000, 0.1 M MES BUFFER, PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.17 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.675 α = 90 b = 84.061 β = 98.87 c = 98.665 γ = 90
Symmetry Space Group P 1 21 1
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 OXFORD INSTRUMENTS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 95.35 87.3 0.12 7.6 2.8 45379
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.47 78.2 0.69 2.2 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 PDB ENTRY 1EGU 2.8 95.35 29209 1517 88.5 0.231 0.229 0.2345 0.277 0.2225 RANDOM 30.87
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] -1.52 0.03 -1 2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.749 r_dihedral_angle_4_deg 20.991 r_dihedral_angle_3_deg 13.191 r_scangle_it 5.203 r_mcangle_it 4.529 r_angle_other_deg 3.614 r_scbond_it 3.487 r_mcbond_it 2.48 r_angle_refined_deg 1.587 r_dihedral_angle_1_deg 1.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.749 r_dihedral_angle_4_deg 20.991 r_dihedral_angle_3_deg 13.191 r_scangle_it 5.203 r_mcangle_it 4.529 r_angle_other_deg 3.614 r_scbond_it 3.487 r_mcbond_it 2.48 r_angle_refined_deg 1.587 r_dihedral_angle_1_deg 1.393 r_symmetry_hbond_refined 0.369 r_symmetry_vdw_other 0.357 r_nbd_other 0.27 r_symmetry_vdw_refined 0.266 r_nbd_refined 0.24 r_nbtor_refined 0.198 r_xyhbond_nbd_refined 0.155 r_nbtor_other 0.111 r_chiral_restr 0.106 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11582 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing