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Structure of muramidase from Acremonium alcalophilum
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, SITTING DROP 293 0.2M NaCl, 0.1M phosphate/citrate pH 4.2, 20% W/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.98 37.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.087 α = 90 b = 77.272 β = 104.195 c = 35.728 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 PIXEL DECTRIS PILATUS3 S 6M 2017-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.65 Diamond I24
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 0.78 38.64 99.1 0.979 5.4 3.9 201033
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 0.78 0.79 0.356
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 0.78 38.636 200983 10021 99.049 0.122 0.1216 0.1211 0.1337 0.1333 9.599
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] -0.034 0.088 -0.122 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.988 r_dihedral_angle_4_deg 19.902 r_rigid_bond_restr 15.837 r_dihedral_angle_3_deg 11.856 r_dihedral_angle_1_deg 7.298 r_mcbond_other 7.217 r_mcbond_it 7.215 r_mcangle_it 6.788 r_mcangle_other 6.786 r_lrange_it 6.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.988 r_dihedral_angle_4_deg 19.902 r_rigid_bond_restr 15.837 r_dihedral_angle_3_deg 11.856 r_dihedral_angle_1_deg 7.298 r_mcbond_other 7.217 r_mcbond_it 7.215 r_mcangle_it 6.788 r_mcangle_other 6.786 r_lrange_it 6.306 r_lrange_other 5.668 r_scangle_it 4.947 r_scangle_other 4.947 r_scbond_other 3.345 r_scbond_it 3.34 r_angle_refined_deg 1.98 r_angle_other_deg 1.826 r_xyhbond_nbd_refined 0.358 r_symmetry_nbd_refined 0.273 r_symmetry_xyhbond_nbd_refined 0.258 r_nbd_other 0.229 r_nbd_refined 0.216 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.195 r_chiral_restr 0.115 r_symmetry_nbtor_other 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_symmetry_xyhbond_nbd_other 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1636 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing