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Hydrolytic potential of the ammonia-oxidizing Thaumarchaeon Nitrososphaera gargenis - crystal structure and activity profiles of carboxylesterases linked to their metabolic function
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A88 PDB ENTRY 1A88
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2 M MAGNESIUM ACETATE, 20% PEG 3350, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.947 α = 90 b = 65.461 β = 104.17 c = 84.591 γ = 90
Symmetry Space Group I 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) PETRA III, EMBL c/o DESY P14 (MX2)
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 1.5 51.2 99 0.03 7.3 3.3 42828 2
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 1.5 1.6 99 0.17 21.2 3.4
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 1A88 1.5 51.16 40671 2156 99.15 0.14269 0.14159 0.1534 0.16309 0.1716 RANDOM 16.613
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] 0.1 -0.07 0.1 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.878 r_dihedral_angle_4_deg 16.531 r_dihedral_angle_3_deg 12.025 r_dihedral_angle_1_deg 5.412 r_scbond_it 2.715 r_mcangle_it 2.49 r_angle_refined_deg 1.978 r_mcbond_it 1.613 r_mcbond_other 1.593 r_angle_other_deg 0.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.878 r_dihedral_angle_4_deg 16.531 r_dihedral_angle_3_deg 12.025 r_dihedral_angle_1_deg 5.412 r_scbond_it 2.715 r_mcangle_it 2.49 r_angle_refined_deg 1.978 r_mcbond_it 1.613 r_mcbond_other 1.593 r_angle_other_deg 0.916 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2151 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing