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Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.15 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 30.0% polyethylene glycol 1500, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2 38.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.349 α = 90 b = 63.713 β = 90 c = 72.962 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 PIXEL DECTRIS PILATUS 6M Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator 2012-07-16 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 SSRL BL12-2
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 1.15 28.666 92.1 0.067 12.95 71198 -3 11.453
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 1.15 1.19 60.2 0.883 1.84 13.15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.15 28.666 71147 3572 91.92 0.1323 0.1306 0.1396 0.164 0.17 RANDOM 18.3283
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] 0.1 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.773 r_dihedral_angle_4_deg 18.843 r_dihedral_angle_3_deg 12.434 r_sphericity_free 11.227 r_scangle_it 6.496 r_sphericity_bonded 6.305 r_dihedral_angle_1_deg 6.07 r_scbond_it 4.721 r_mcangle_it 3.871 r_mcbond_it 2.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.773 r_dihedral_angle_4_deg 18.843 r_dihedral_angle_3_deg 12.434 r_sphericity_free 11.227 r_scangle_it 6.496 r_sphericity_bonded 6.305 r_dihedral_angle_1_deg 6.07 r_scbond_it 4.721 r_mcangle_it 3.871 r_mcbond_it 2.746 r_mcbond_other 2.527 r_rigid_bond_restr 2.234 r_angle_refined_deg 1.756 r_angle_other_deg 1.006 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1840 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing