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Crystal structure of Streptococcus Pneumoniae Hyaluronate Lyase from 70percent saturated malonate.
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 7.6 pH 7.60
Crystal Properties Matthews coefficient Solvent content 2.56 51.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.722 α = 90 b = 101.052 β = 125.12 c = 85.211 γ = 90
Symmetry Space Group C 1 2 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 3.3 69.01 93.8 0.17 6.3 4.8 11046
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 3.3 3.48 84 0.61 2.3 5
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EGU 3.3 69.01 11046 578 93.8 0.302 0.301 0.327 RANDOM 51.86
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] 11.52 9.09 -5.77 4.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.236 r_dihedral_angle_3_deg 24.471 r_dihedral_angle_4_deg 21.066 r_dihedral_angle_1_deg 6.902 r_angle_other_deg 3.825 r_scangle_it 1.331 r_angle_refined_deg 1.08 r_mcangle_it 0.875 r_scbond_it 0.7 r_mcbond_it 0.466
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.236 r_dihedral_angle_3_deg 24.471 r_dihedral_angle_4_deg 21.066 r_dihedral_angle_1_deg 6.902 r_angle_other_deg 3.825 r_scangle_it 1.331 r_angle_refined_deg 1.08 r_mcangle_it 0.875 r_scbond_it 0.7 r_mcbond_it 0.466 r_symmetry_hbond_refined 0.251 r_symmetry_vdw_other 0.231 r_nbd_other 0.22 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.211 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.132 r_nbtor_other 0.111 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 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 5734 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing