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Crystal structure of a Glycoside hydrolase family protein (Rv0315 ortholog) from Mycobacterium thermorestibile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RQ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 MythA.18623.a.B2.PS02026 at 20.8 mg/mL against JCSG+ screen condition G5, 5 mM CoCl2, 5 mM CdCl2, 5 mM MgCl2, 5 mM NiCl2, 0.1 M Hepes pH 7.5, 15% PEG 3350 supplemented with 20 % EG as cryo
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.55 α = 90 b = 74.55 β = 90 c = 95.53 γ = 90
Symmetry Space Group P 43 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 300 mm CCD 2014-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.35 50 100 0.059 0.061 28.25 14.4 59755 -3 18.076
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.39 100 0.532 0.552 5.4 14.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3rq0 1.35 50 56708 2968 99.97 0.1264 0.1253 0.1479 0.1636 RANDOM 14.451
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] -0.56 -0.56 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.355 r_dihedral_angle_4_deg 24.391 r_dihedral_angle_3_deg 9.765 r_dihedral_angle_1_deg 7.272 r_sphericity_bonded 5.883 r_rigid_bond_restr 1.703 r_angle_refined_deg 1.361 r_mcangle_it 1.227 r_mcbond_it 0.961 r_mcbond_other 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.355 r_dihedral_angle_4_deg 24.391 r_dihedral_angle_3_deg 9.765 r_dihedral_angle_1_deg 7.272 r_sphericity_bonded 5.883 r_rigid_bond_restr 1.703 r_angle_refined_deg 1.361 r_mcangle_it 1.227 r_mcbond_it 0.961 r_mcbond_other 0.96 r_angle_other_deg 0.739 r_chiral_restr 0.085 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1895 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 26
Software Software Software Name Purpose XDS data reduction REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling BALBES phasing