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Crystal structure of MSMEG_1712 from Mycobacterium smegmatis in complex with alpha-L-arabinofuranose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HB0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1 M Tris, pH 8.0
21 % PEG 400
0.325 M NaOAc
0.1 M NaCl
Crystal Properties Matthews coefficient Solvent content 3.1 60.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.5 α = 90 b = 119.5 β = 90 c = 234.77 γ = 90
Symmetry Space Group I 41 2 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 PIXEL DECTRIS EIGER X 16M 2018-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.75 106.5 92.9 17.5 25.7 63068 109.79
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 2.75 3.19
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6HB0 2.76 28.95 11270 522 50.5 0.221 0.218 0.2452 0.279 0.3022 RANDOM 96.95
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] -3.4155 -3.4155 6.831
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.82 t_omega_torsion 2.83 t_angle_deg 1.15 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.82 t_omega_torsion 2.83 t_angle_deg 1.15 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4207 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 32
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling PHASER phasing