☰ Navigation Tabs
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, HANGING DROP 279.15 0.05 M Sodium acetate: Acetic acid pH 5.4, 0.8/1.2 M NaH2PO4/K2HPO4
Crystal Properties Matthews coefficient Solvent content 2.69 54.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.71 α = 90 b = 117.71 β = 90 c = 98.987 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 RIGAKU HyPix-3000 2025-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.68 12.716 99.1 0.047 0.191 0.047 0.996 12.7 2 48016 24402 10.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 2.77 100 0.372 0.97
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 2.68 12.716 19859 1009 98.816 0.191 0.1876 0.1946 0.2477 0.2531 11.846
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] 1.097 1.097 -2.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.875 r_dihedral_angle_6_deg 16.024 r_dihedral_angle_2_deg 7.758 r_dihedral_angle_1_deg 6.658 r_lrange_other 5.939 r_lrange_it 5.876 r_scangle_it 3.032 r_scangle_other 3.031 r_mcangle_it 2.188 r_mcangle_other 2.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.875 r_dihedral_angle_6_deg 16.024 r_dihedral_angle_2_deg 7.758 r_dihedral_angle_1_deg 6.658 r_lrange_other 5.939 r_lrange_it 5.876 r_scangle_it 3.032 r_scangle_other 3.031 r_mcangle_it 2.188 r_mcangle_other 2.188 r_scbond_it 1.752 r_scbond_other 1.752 r_angle_refined_deg 1.351 r_mcbond_it 1.238 r_mcbond_other 1.237 r_dihedral_angle_other_2_deg 1.105 r_angle_other_deg 0.444 r_nbd_refined 0.222 r_metal_ion_refined 0.205 r_symmetry_nbd_other 0.196 r_nbd_other 0.182 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.169 r_symmetry_nbd_refined 0.167 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4089 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MrBUMP phasing