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GH24 family muramidase from Trichophaea saccata with an SH3-like cell wall binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 AmSO4 screen (Qiagen), condition C3:
0.2 M potassium fluoride, 2.2 M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 1.84 33.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.438 α = 90 b = 99.438 β = 90 c = 133.254 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS 6M 2014-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.94 46.582 100 0.073 0.083 0.04 0.999 16.2 8.2 56987 32.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.99 100 2.263 2.582 1.232 0.328 0.9 8.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1HDE 1.94 46.582 56937 2862 99.981 0.17 0.168 0.1766 0.2013 0.2088 40.867
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] 0.129 0.064 0.129 -0.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.64 r_dihedral_angle_3_deg 12.278 r_dihedral_angle_2_deg 6.594 r_lrange_it 6.234 r_dihedral_angle_1_deg 6.212 r_lrange_other 6.158 r_scangle_it 4.906 r_scangle_other 4.905 r_scbond_it 4.192 r_scbond_other 4.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.64 r_dihedral_angle_3_deg 12.278 r_dihedral_angle_2_deg 6.594 r_lrange_it 6.234 r_dihedral_angle_1_deg 6.212 r_lrange_other 6.158 r_scangle_it 4.906 r_scangle_other 4.905 r_scbond_it 4.192 r_scbond_other 4.191 r_mcangle_it 3.222 r_mcangle_other 3.221 r_mcbond_other 2.512 r_mcbond_it 2.511 r_angle_refined_deg 1.54 r_angle_other_deg 0.536 r_metal_ion_refined 0.401 r_nbd_refined 0.206 r_nbd_other 0.204 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.142 r_symmetry_nbd_refined 0.118 r_chiral_restr 0.077 r_symmetry_nbtor_other 0.073 r_ncsr_local_group_1 0.066 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3610 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 2
Software Software Software Name Purpose XDS data reduction xia2 data reduction Aimless data scaling BALBES phasing REFMAC refinement