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NAD(P)-dependent oxidoreductase from Kutzneria albida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JKU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 279.15 1.0 M Ammonium Sulfate, 0.1 M HEPES:NaOH pH 7.0, and 0.5% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.395 α = 90 b = 117.395 β = 90 c = 99.569 γ = 90
Symmetry Space Group P 43 21 2
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 2025-01-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.499 45.84 98.9 0.057 0.995 13.3 1.9 24403
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.499 2.59 0.813
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.499 41.54 24401 1270 98.854 0.164 0.1603 0.1681 0.2275 0.2282 37.351
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] -0.005 -0.005 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.312 r_dihedral_angle_3_deg 15.974 r_lrange_other 9.015 r_lrange_it 8.992 r_dihedral_angle_2_deg 8.065 r_scangle_it 7.751 r_scangle_other 7.632 r_dihedral_angle_1_deg 6.598 r_mcangle_it 5.504 r_mcangle_other 5.504
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.312 r_dihedral_angle_3_deg 15.974 r_lrange_other 9.015 r_lrange_it 8.992 r_dihedral_angle_2_deg 8.065 r_scangle_it 7.751 r_scangle_other 7.632 r_dihedral_angle_1_deg 6.598 r_mcangle_it 5.504 r_mcangle_other 5.504 r_scbond_it 5.14 r_scbond_other 5.068 r_mcbond_it 3.874 r_mcbond_other 3.873 r_angle_refined_deg 1.552 r_dihedral_angle_other_2_deg 0.793 r_angle_other_deg 0.508 r_nbd_refined 0.237 r_symmetry_nbd_other 0.198 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.182 r_nbd_other 0.172 r_symmetry_nbd_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4086 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction Aimless data scaling MrBUMP phasing