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Crystal structure of apo Adenylosuccinate Lyase from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VD6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Under Oil, Microbatch Method 7.5 291 0.1M Na HEPES pH 7.5, 1.4M sodium citrate, 0.1M betaine hydrochloride, Under Oil, Microbatch Method, temperature 291.0K
Crystal Properties Matthews coefficient Solvent content 2.27 45.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.6 α = 90 b = 176.83 β = 90 c = 73.3 γ = 90
Symmetry Space Group P 21 21 2
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 225 mm CCD Bent collimating mirror and toroid 2011-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9537 ESRF BM14
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 2.16 37.86 0.083 11.3 4.85 52292 49552 26.371
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 2.16 2.28 0.27 14.2 4.2 7312
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2VD6 2.16 37.86 52292 49552 2661 98.64 0.20642 0.20475 0.2106 0.23829 0.2374 RANDOM 31.547
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] 0.08 -0.17 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.468 r_dihedral_angle_3_deg 12.596 r_dihedral_angle_4_deg 12.396 r_dihedral_angle_1_deg 4.349 r_long_range_B_refined 3.433 r_long_range_B_other 3.226 r_mcangle_it 0.922 r_mcangle_other 0.921 r_angle_refined_deg 0.759 r_angle_other_deg 0.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.468 r_dihedral_angle_3_deg 12.596 r_dihedral_angle_4_deg 12.396 r_dihedral_angle_1_deg 4.349 r_long_range_B_refined 3.433 r_long_range_B_other 3.226 r_mcangle_it 0.922 r_mcangle_other 0.921 r_angle_refined_deg 0.759 r_angle_other_deg 0.686 r_scangle_other 0.576 r_mcbond_it 0.492 r_mcbond_other 0.492 r_scbond_it 0.294 r_scbond_other 0.294 r_chiral_restr 0.039 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6912 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling