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Crystal structure of a Putative oxidoreductase from Mycobacterium avium 104
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VPD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 MyavA.01379.a.A1 22.39 mg/ml, 20% PEG 6000, 0.1 M Hepes pH 7.0, 0.2M CaCl2, cryo-protectant 25% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.41 49.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.055 α = 90 b = 76.829 β = 90 c = 115.879 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97 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 2.25 50 100 0.105 7.3 7.2 29158
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 2.25 2.32 100 0.649 7.3 2415
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 1VPD 2.25 50 28979 1475 99.5 0.2013 0.1995 0.2067 0.2338 0.2353 RANDOM 28.4089
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] 0.53 -1.22 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.036 r_dihedral_angle_4_deg 14.598 r_dihedral_angle_3_deg 13.206 r_dihedral_angle_1_deg 5.34 r_scangle_it 1.042 r_angle_refined_deg 0.916 r_angle_other_deg 0.841 r_scbond_it 0.598 r_mcangle_it 0.428 r_mcbond_it 0.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.036 r_dihedral_angle_4_deg 14.598 r_dihedral_angle_3_deg 13.206 r_dihedral_angle_1_deg 5.34 r_scangle_it 1.042 r_angle_refined_deg 0.916 r_angle_other_deg 0.841 r_scbond_it 0.598 r_mcangle_it 0.428 r_mcbond_it 0.224 r_chiral_restr 0.053 r_mcbond_other 0.026 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3968 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction