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Crystal structure of the zeamine pathway ketoreductase Zmn13-KR, in complex with NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 0.1 M HEPES, 10% (v/v) isopropanol, 5% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.14 42.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.342 α = 90 b = 109.321 β = 90 c = 208.278 γ = 90
Symmetry Space Group C 2 2 21
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 9M 2025-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
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 1.9 64.74 97.7 0.103 0.118 0.056 0.996 7.2 3.9 70494 26.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 95.3 0.577 0.668 0.327 0.748 1.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 64.739 70468 3536 97.266 0.186 0.1844 0.1844 0.2246 0.2246 RANDOM 31.741
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] -0.009 0.009 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.612 r_dihedral_angle_3_deg 13.542 r_lrange_it 7.405 r_dihedral_angle_2_deg 7.105 r_dihedral_angle_1_deg 6.375 r_scangle_it 5.606 r_scbond_it 3.772 r_mcangle_it 3.74 r_mcbond_it 2.553 r_angle_refined_deg 1.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.612 r_dihedral_angle_3_deg 13.542 r_lrange_it 7.405 r_dihedral_angle_2_deg 7.105 r_dihedral_angle_1_deg 6.375 r_scangle_it 5.606 r_scbond_it 3.772 r_mcangle_it 3.74 r_mcbond_it 2.553 r_angle_refined_deg 1.454 r_nbtor_refined 0.306 r_symmetry_nbd_refined 0.238 r_nbd_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.195 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.103 r_ncsr_local_group_5 0.088 r_ncsr_local_group_6 0.087 r_ncsr_local_group_4 0.083 r_ncsr_local_group_1 0.079 r_ncsr_local_group_3 0.079 r_ncsr_local_group_2 0.077 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7203 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 208
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing