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Crystal structure of nitrilotriacetate monooxygenase component B (A0R521 homolog) from Mycobacterium thermoresistibile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RZ0 PDB entry 1rz0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 68.9 mg/mL protein against PACT screen condition B10, 0.2 M MgCl2, 0.1 M MES pH 6.0,
20% PEG 6000 with 20% glycerol as cryo-protectant, crystal tracking ID 215735b10, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.96 37.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.45 α = 90 b = 91.02 β = 90 c = 165.64 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 2010-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 1.6 50 99.8 0.095 14.4 14.5 97543 97350 -3 20.998
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 1.6 1.64 99.9 0.428 5.4 13.7
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 1rz0 1.6 19.56 97026 4857 99.48 0.188 0.1864 0.1874 0.2175 0.2173 RANDOM 16.7061
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 0.19 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.408 r_dihedral_angle_4_deg 17.473 r_dihedral_angle_3_deg 11.01 r_dihedral_angle_1_deg 6.557 r_scangle_it 3.33 r_scbond_it 2.017 r_mcangle_it 1.346 r_angle_refined_deg 1.273 r_mcbond_it 0.738 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.408 r_dihedral_angle_4_deg 17.473 r_dihedral_angle_3_deg 11.01 r_dihedral_angle_1_deg 6.557 r_scangle_it 3.33 r_scbond_it 2.017 r_mcangle_it 1.346 r_angle_refined_deg 1.273 r_mcbond_it 0.738 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5541 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 6
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction