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R-imine reductase from Streptomyces kanamyceticus in complex with NADP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YB4 PDB ENTRY 1YB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 35% (V/V) TASCIMATE PH 7.0 WITH 2.5% (V/V) ETHYLENE GLYCOL. 10 MG ML-1 PROTEIN. CRYSTALS WERE SOAKED WITH MOTHER LIQUOR CONTAINING 10 MM NADPH PRIOR TO FLASH COOLING
Crystal Properties Matthews coefficient Solvent content 4 69.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 205.79 α = 90 b = 130.31 β = 107.08 c = 77.7 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 120 CCD ADSC CCD 2012-07-29 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 2.73 74.27 99.4 0.08 12.2 4.3 51705 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 2.73 2.8 99.1 0.6 2 4.3
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 1YB4 2.73 74.27 49076 2629 99.26 0.18681 0.18521 0.1948 0.21649 0.2238 RANDOM 55.823
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] -0.68 -1.37 5.94 -4.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.915 r_dihedral_angle_4_deg 21.276 r_dihedral_angle_3_deg 16.902 r_dihedral_angle_1_deg 6.61 r_angle_refined_deg 1.79 r_angle_other_deg 1.147 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.915 r_dihedral_angle_4_deg 21.276 r_dihedral_angle_3_deg 16.902 r_dihedral_angle_1_deg 6.61 r_angle_refined_deg 1.79 r_angle_other_deg 1.147 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it 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 8091 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling BALBES phasing