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Catalytic domain of N1356
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9XV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% (v/v) PEG 3350, 0.04M citric acid, 0.06M Bis-Tris propane (pH 6.4)
Crystal Properties Matthews coefficient Solvent content 2.02 39.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.057 α = 90 b = 78.09 β = 113.99 c = 40.222 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 EIGER X 9M 2024-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
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 1.2 33.68 98.9 0.056 0.999 18.9 6.3 69717
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 1.2 1.243 0.27 0.947 4.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.2 33.68 66310 3572 98.59 0.13995 0.13934 0.1493 0.15109 0.1602 RANDOM 11.429
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] -0.08 -0.48 0.55 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.402 r_dihedral_angle_2_deg 8.502 r_dihedral_angle_1_deg 6.404 r_scangle_other 2.73 r_scbond_other 2.026 r_scbond_it 2.02 r_angle_refined_deg 1.912 r_mcangle_it 1.169 r_mcangle_other 1.168 r_mcbond_it 0.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.402 r_dihedral_angle_2_deg 8.502 r_dihedral_angle_1_deg 6.404 r_scangle_other 2.73 r_scbond_other 2.026 r_scbond_it 2.02 r_angle_refined_deg 1.912 r_mcangle_it 1.169 r_mcangle_other 1.168 r_mcbond_it 0.829 r_mcbond_other 0.827 r_angle_other_deg 0.667 r_chiral_restr 0.116 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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_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 1926 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction