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Crystal structure of Molybdopterin biosynthesis mog protein from Mycobacterium paratuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OI9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 290 Internal tracking number 217822A1. PACT screen
condition A1: SPG buffer, pH 4, 25% PEG1500, with protein (MypaA.00778.b.A1 PW29403) at 24.39 mg/ml, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.2 44.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.65 α = 90 b = 68.65 β = 90 c = 52.83 γ = 120
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 315 2010-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976504 ALS 5.0.3
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 1.8 19.75 99.3 0.042 24.39 5.48889 13236 13146 -3 33.133
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 1.8 1.85 99.6 0.519 3.3 5.544979 960
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT 3OI9 1.8 19.75 13236 13128 646 99.18 0.195 0.195 0.193 0.2049 0.228 0.2392 RANDOM 26.401
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] 0.7 0.35 0.7 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.919 r_dihedral_angle_3_deg 13.59 r_dihedral_angle_4_deg 12.212 r_dihedral_angle_1_deg 5.258 r_scangle_it 4.029 r_scbond_it 2.425 r_angle_refined_deg 1.566 r_mcangle_it 1.507 r_angle_other_deg 0.989 r_mcbond_it 0.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.919 r_dihedral_angle_3_deg 13.59 r_dihedral_angle_4_deg 12.212 r_dihedral_angle_1_deg 5.258 r_scangle_it 4.029 r_scbond_it 2.425 r_angle_refined_deg 1.566 r_mcangle_it 1.507 r_angle_other_deg 0.989 r_mcbond_it 0.922 r_mcbond_other 0.274 r_chiral_restr 0.092 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1024 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 5
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction REFMAC phasing