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Structure of muramidase from Trichobolus zukalii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X8R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 lithium sulphate, ammonium sulphate, sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.29 46.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.398 α = 97.076 b = 48.582 β = 99.531 c = 55.737 γ = 98.15
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 0.98 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.4 27.187 93.8 0.992 15.8 2.1 73721
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.436 0.956
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 2X8R 1.4 27.17 73721 3758 93.765 0.106 0.1041 0.1041 0.1427 0.1428 9.194
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] -0.098 0.097 -0.075 0.391 -0.217 -0.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.957 r_dihedral_angle_4_deg 11.325 r_dihedral_angle_3_deg 10.961 r_dihedral_angle_1_deg 6.899 r_lrange_it 4.577 r_lrange_other 3.358 r_scangle_it 2.717 r_scangle_other 2.637 r_rigid_bond_restr 2.609 r_scbond_it 2.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.957 r_dihedral_angle_4_deg 11.325 r_dihedral_angle_3_deg 10.961 r_dihedral_angle_1_deg 6.899 r_lrange_it 4.577 r_lrange_other 3.358 r_scangle_it 2.717 r_scangle_other 2.637 r_rigid_bond_restr 2.609 r_scbond_it 2.236 r_scbond_other 2.187 r_angle_refined_deg 1.909 r_angle_other_deg 1.744 r_mcangle_it 1.727 r_mcangle_other 1.727 r_mcbond_it 1.387 r_mcbond_other 1.387 r_symmetry_nbd_refined 0.309 r_xyhbond_nbd_refined 0.298 r_nbd_refined 0.245 r_nbd_other 0.24 r_symmetry_xyhbond_nbd_refined 0.205 r_nbtor_refined 0.196 r_symmetry_nbd_other 0.19 r_chiral_restr 0.115 r_symmetry_nbtor_other 0.091 r_ncsr_local_group_1 0.071 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3167 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing