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Crystal structure of a putative uncharacterized protein from Mycobacterium Paratuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other STRUCTURE SOLVED VIA IODIDE PHASING AT CUKALPHA, DATA SET 2 WAS USED FOR THIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 EMERALDBIOSYSTEMS JCSG+ SCREEN B4: 100MM HEPES PH 7.5, 10% PEG 8000, 8% ETHYLENE GLYCOL, MYPAA.01249.CA1 PW29465 AT 29 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K. 2 VAPOR DIFFUSION, SITTING DROP 7.5 290 EMERALDBIOSYSTEMS JCSG+ SCREEN B4: 100MM HEPES PH 7.5, 10% PEG 8000, 8% ETHYLENE GLYCOL, MYPAA.01249.CA1 PW29465 AT 29 MG/ML, FOR PHASING THIS CRYSTAL WAS TRANFERRED IN 100MM HEPES PH 7.5, 15% PEG 6000, 10% ETHYLENE GLYCOL, 400MM SODIUM IODIDE, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.92 α = 90 b = 78.1 β = 90 c = 86.22 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 300 mm CCD 2011-03-04 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD RIGAKU SATURN 944+ 2011-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.978560 APS 21-ID-G 2 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1,2 1.5 50 98.9 0.049 0.049 22.61 7.6 70109 70109 -3 22.7
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) 1,2 1.5 1.54 100 0.389 0.389 4.4 5.4 5161
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 STRUCTURE SOLVED VIA IODIDE PHASING AT CUKALPHA, DATA SET 2 WAS USED FOR THIS 1.5 49.92 70109 69906 3526 98.7 0.134 0.134 0.133 0.1343 0.15 0.151 RANDOM 14.71
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] -0.19 0.62 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.377 r_dihedral_angle_4_deg 17.028 r_dihedral_angle_3_deg 11.658 r_dihedral_angle_1_deg 5.525 r_scangle_it 4.028 r_scbond_it 2.491 r_mcangle_it 1.562 r_angle_refined_deg 1.539 r_angle_other_deg 1.019 r_mcbond_it 0.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.377 r_dihedral_angle_4_deg 17.028 r_dihedral_angle_3_deg 11.658 r_dihedral_angle_1_deg 5.525 r_scangle_it 4.028 r_scbond_it 2.491 r_mcangle_it 1.562 r_angle_refined_deg 1.539 r_angle_other_deg 1.019 r_mcbond_it 0.924 r_mcbond_other 0.259 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2031 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 19
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling