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Crystal structure of Laterosporulin10, bacteriocin produced by Brevibacillus sp. strain SKDU10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OZK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1 M calcium chloride, 0.1 M sodium cacodylate pH 5.5, 12 % PEG w/v 8000 and 3 % w/v Trimethylamine N-oxide dihydrate
Crystal Properties Matthews coefficient Solvent content 1.57 21.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 22.28 α = 110.62 b = 29.34 β = 89.99 c = 32.15 γ = 104.94
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2017-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.2 29.94 94.1 0.111 0.141 0.087 6.5 2.5 3487
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 90.3 0.493 0.493 0.628 0.384 1.5 2.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4OZK 2.2 29.94 3486 363 94.09 0.2237 0.2237 0.2174 0.2579 0.2627 40.091
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] -2.82 1.21 0.57 1.47 1.28 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.486 r_dihedral_angle_3_deg 16.79 r_dihedral_angle_4_deg 13.72 r_dihedral_angle_1_deg 5.725 r_angle_refined_deg 2.184 r_chiral_restr 0.09 r_bond_refined_d 0.021 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 842 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing