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Crystal structure of Cph001-D189N in complex with CMN IIA and ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8I80
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 Sodium acetate trihydrate,
Polyethylene glycol 4,000,
Glycerol
Crystal Properties Matthews coefficient Solvent content 2.59 52.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.288 α = 90 b = 87.074 β = 90 c = 87.951 γ = 90
Symmetry Space Group P 21 21 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 CCD RAYONIX MX300HE 2022-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3 30 99.9 0.145 15.3 7.2 13117
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 100 0.499 4.5 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3 26.18 11643 946 95.76 0.21638 0.21187 0.2158 0.27493 0.2826 RANDOM 59.332
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] -0.41 -0.01 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.289 r_dihedral_angle_1_deg 4.624 r_long_range_B_refined 3.298 r_long_range_B_other 3.298 r_mcangle_it 1.793 r_mcangle_other 1.793 r_dihedral_angle_2_deg 1.536 r_scangle_other 1.164 r_mcbond_it 0.966 r_mcbond_other 0.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.289 r_dihedral_angle_1_deg 4.624 r_long_range_B_refined 3.298 r_long_range_B_other 3.298 r_mcangle_it 1.793 r_mcangle_other 1.793 r_dihedral_angle_2_deg 1.536 r_scangle_other 1.164 r_mcbond_it 0.966 r_mcbond_other 0.966 r_angle_refined_deg 0.658 r_scbond_it 0.619 r_scbond_other 0.619 r_angle_other_deg 0.617 r_chiral_restr 0.03 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.002 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 4267 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 31
Software Software Software Name Purpose SCALA data scaling REFMAC refinement HKL-2000 data reduction MOLREP phasing