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Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.07 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H4J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 30.00% polyethylene glycol 1500, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.03 39.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.473 α = 90 b = 63.552 β = 90 c = 73.997 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 325 mm CCD Vertical focusing mirror; double crystal Si(111) monochromator 2014-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 SSRL BL14-1
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 1.07 46.47 95.9 0.034 22.87 3.93 93219 -3 11.481
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 1.07 1.11 85 0.34 3 2.97
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4H4J 1.07 39.355 93156 4687 95.88 0.1117 0.1103 0.1377 0.1502 RANDOM 12.8506
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] -0.09 -0.18 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.093 r_sphericity_free 21.348 r_dihedral_angle_4_deg 16.499 r_dihedral_angle_3_deg 11.589 r_sphericity_bonded 6.812 r_dihedral_angle_1_deg 5.728 r_angle_refined_deg 1.362 r_rigid_bond_restr 1.255 r_mcangle_it 1.095 r_mcbond_it 0.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.093 r_sphericity_free 21.348 r_dihedral_angle_4_deg 16.499 r_dihedral_angle_3_deg 11.589 r_sphericity_bonded 6.812 r_dihedral_angle_1_deg 5.728 r_angle_refined_deg 1.362 r_rigid_bond_restr 1.255 r_mcangle_it 1.095 r_mcbond_it 0.812 r_mcbond_other 0.788 r_angle_other_deg 0.774 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1831 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms 18
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction XSCALE data scaling REFMAC refinement XDS data reduction MOLREP phasing