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Crystal structure of native Msmeg3575 deaminase from Mycobacterium smegmatis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate tri-hydrate pH 6.0 and 15% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.262 α = 90 b = 108.335 β = 90 c = 53.261 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 2016-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.28 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.89 47.8 99.8 0.073 73 39.8 29961
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 2 99.3
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 1.89 47.8 27732 1988 99.3 0.141 0.138 0.1529 0.178 0.1877 RANDOM 16.09
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.851 r_dihedral_angle_4_deg 20.132 r_dihedral_angle_3_deg 13.654 r_long_range_B_refined 6.701 r_long_range_B_other 6.573 r_dihedral_angle_1_deg 5.684 r_scangle_other 4.308 r_scbond_it 2.842 r_scbond_other 2.841 r_mcangle_it 2.444
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.851 r_dihedral_angle_4_deg 20.132 r_dihedral_angle_3_deg 13.654 r_long_range_B_refined 6.701 r_long_range_B_other 6.573 r_dihedral_angle_1_deg 5.684 r_scangle_other 4.308 r_scbond_it 2.842 r_scbond_other 2.841 r_mcangle_it 2.444 r_mcangle_other 2.444 r_angle_refined_deg 1.872 r_mcbond_it 1.742 r_mcbond_other 1.697 r_angle_other_deg 1.092 r_chiral_restr 0.121 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2379 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELXCD phasing