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Structure of Imine Reductase BcSIRED from Bacillus cereus BAG3X2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZGY PDB ENTRY 3ZGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 25% (W/V) PEG 3350; 0.2M MGCL2; 0.1M HEPES PH 7.5; PROTEIN AT 50 MG ML-1
Crystal Properties Matthews coefficient Solvent content 3.1 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.777 α = 90 b = 59.593 β = 90 c = 214.867 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 120 PIXEL DECTRIS PILATUS 6M 2014-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.71 32.45 99.1 0.06 17.7 6.6 77781 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 1.71 1.74 96.8 0.6 2.6 6.1
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 3ZGY 1.71 107.43 73921 3775 98.91 0.17959 0.17805 0.1885 0.20988 0.2211 RANDOM 22.861
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] -0.11 1.05 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.916 r_dihedral_angle_4_deg 23.064 r_dihedral_angle_3_deg 13.28 r_dihedral_angle_1_deg 5.456 r_scbond_it 3.461 r_mcangle_it 2.684 r_angle_refined_deg 2.061 r_mcbond_it 2.014 r_mcbond_other 2.014 r_angle_other_deg 1.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.916 r_dihedral_angle_4_deg 23.064 r_dihedral_angle_3_deg 13.28 r_dihedral_angle_1_deg 5.456 r_scbond_it 3.461 r_mcangle_it 2.684 r_angle_refined_deg 2.061 r_mcbond_it 2.014 r_mcbond_other 2.014 r_angle_other_deg 1.459 r_chiral_restr 0.123 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 4349 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement xia2 data reduction SCALA data scaling MOLREP phasing