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Crystal structure of a murein peptide ligase mpl (psyc_0032) from psychrobacter arcticus 273-4 at 1.65 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2000M NaOAc, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.13 42.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.452 α = 90 b = 52.755 β = 98.47 c = 89.986 γ = 90
Symmetry Space Group C 1 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 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-03-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97932,0.97920 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.65 29.025 100 0.076 0.076 7.479 3.3 59026 17.41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.69 100 0.512 0.512 1.5 3.3 4316
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.65 29.025 59024 2985 99.94 0.156 0.154 0.187 0.1901 RANDOM 16.063
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] -0.42 -0.53 0.98 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.969 r_dihedral_angle_4_deg 17.761 r_dihedral_angle_3_deg 11.151 r_scangle_it 6.005 r_dihedral_angle_1_deg 5.083 r_scbond_it 4.259 r_mcangle_it 2.841 r_mcbond_it 1.838 r_angle_refined_deg 1.594 r_angle_other_deg 0.973
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.969 r_dihedral_angle_4_deg 17.761 r_dihedral_angle_3_deg 11.151 r_scangle_it 6.005 r_dihedral_angle_1_deg 5.083 r_scbond_it 4.259 r_mcangle_it 2.841 r_mcbond_it 1.838 r_angle_refined_deg 1.594 r_angle_other_deg 0.973 r_mcbond_other 0.541 r_chiral_restr 0.107 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3619 Nucleic Acid Atoms Solvent Atoms 588 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing