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Crystal structure of a MeaB and Rv1496 ortholog from Mycobacterium thermoresistible bound to GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MD0 PDB ENTRY 3MD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 MythA.00200.a.A1 PS00590 at 42.4 mg/mL with 2 mM GDP against PACT screen condition B10, 0.2 M MgCl2, 0.1 M MES pH 6.0, 20% PEG 6000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 215739b10, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.12 41.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.38 α = 90 b = 106.43 β = 90 c = 134.04 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 ADSC QUANTUM 315r 2010-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 2.4 50 94.8 0.078 17.07 5.3 24555 23270 -3 44.319
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 2.4 2.46 97.8 0.519 3.02
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 PDB ENTRY 3MD0 2.4 50 23269 2369 94.76 0.2296 0.2243 0.2213 0.2773 0.2745 RANDOM 37.3745
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] 0.35 -1.06 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.103 r_dihedral_angle_4_deg 19.92 r_dihedral_angle_3_deg 16.513 r_dihedral_angle_1_deg 5.519 r_angle_refined_deg 1.492 r_angle_other_deg 1.176 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.103 r_dihedral_angle_4_deg 19.92 r_dihedral_angle_3_deg 16.513 r_dihedral_angle_1_deg 5.519 r_angle_refined_deg 1.492 r_angle_other_deg 1.176 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4435 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 57
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction