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Anbu from Hyphomicrobium sp. strain MC1 - SG: C2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298.15 0.01 M cobalt(II) chloride, 0.1 M Tris, 20 % PVP K15. The protein crystallized in presence of the proteasome inhibitor bortezomib.
Crystal Properties Matthews coefficient Solvent content 3.55 65.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 240.22 α = 90 b = 242.15 β = 90.77 c = 107.32 γ = 90
Symmetry Space Group C 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 EIGER X 16M 2017-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 3.2 40 98.8 0.084 9.7 3.8 99540
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 3.2 3.3 98.6 0.562 2
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 5NYF 3.2 20 94184 4957 98.4 0.23715 0.23502 0.2401 0.2787 0.2845 RANDOM 112.126
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] -2.78 0.48 -5.34 8.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.432 r_dihedral_angle_3_deg 12.726 r_dihedral_angle_4_deg 10.129 r_dihedral_angle_1_deg 4.718 r_long_range_B_refined 4.495 r_long_range_B_other 4.495 r_mcangle_it 2.948 r_mcangle_other 2.947 r_scangle_other 1.971 r_mcbond_it 1.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.432 r_dihedral_angle_3_deg 12.726 r_dihedral_angle_4_deg 10.129 r_dihedral_angle_1_deg 4.718 r_long_range_B_refined 4.495 r_long_range_B_other 4.495 r_mcangle_it 2.948 r_mcangle_other 2.947 r_scangle_other 1.971 r_mcbond_it 1.607 r_mcbond_other 1.607 r_scbond_it 1.028 r_scbond_other 1.028 r_angle_refined_deg 0.92 r_angle_other_deg 0.797 r_chiral_restr 0.052 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29869 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing