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NSP14 IN COMPLEX WITH LIGAND MAVDA-K-197
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7R2V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.25 277 8.0% (V/V) 2-PropOH, 0.1 M imidazole pH 7.25
Crystal Properties Matthews coefficient Solvent content 2.45 49.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.35 α = 90 b = 101.492 β = 108.36 c = 90.517 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 X 16M 2025-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.767 65.66 96.6 0.141 0.141 0.152 0.057 0.9927 9.3 7.1 28601
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.767 2.814 100 1.336 1.336 1.436 0.525 0.7239 1.4 7.4
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.77 65.66 27194 1406 96.56 0.20757 0.20542 0.25193 RANDOM 69.843
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] -0.77 2.02 0.71 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.81 r_dihedral_angle_3_deg 12.714 r_dihedral_angle_1_deg 6.078 r_long_range_B_refined 5.954 r_long_range_B_other 5.954 r_mcangle_it 4.143 r_mcangle_other 4.142 r_scangle_other 3.568 r_mcbond_it 2.457 r_mcbond_other 2.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.81 r_dihedral_angle_3_deg 12.714 r_dihedral_angle_1_deg 6.078 r_long_range_B_refined 5.954 r_long_range_B_other 5.954 r_mcangle_it 4.143 r_mcangle_other 4.142 r_scangle_other 3.568 r_mcbond_it 2.457 r_mcbond_other 2.456 r_scbond_it 2.124 r_scbond_other 2.124 r_angle_refined_deg 1.062 r_angle_other_deg 0.458 r_chiral_restr 0.047 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7084 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 135
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data reduction autoPROC data scaling Aimless data scaling REFMAC refinement PHASER phasing PDB_EXTRACT data extraction