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Crystal structure of Cph001-D189N in complex with GTP
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 2.56 51.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.155 α = 90 b = 86.784 β = 90 c = 87.335 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 MX300-HS 2022-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
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 2.23 30 99.5 0.063 0.997 11.03 3.81 29326
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 2.23 2.37 98.6 0.437 0.924 2.36
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 2.23 28.3 29326 1565 99.63 0.23082 0.22779 0.2319 0.28845 0.2872 RANDOM 63.61
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] -0.09 -0.04 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.542 r_long_range_B_refined 7.516 r_long_range_B_other 7.516 r_dihedral_angle_2_deg 6.162 r_dihedral_angle_1_deg 6.043 r_scangle_other 5.286 r_mcangle_it 4.927 r_mcangle_other 4.926 r_scbond_it 3.234 r_scbond_other 3.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.542 r_long_range_B_refined 7.516 r_long_range_B_other 7.516 r_dihedral_angle_2_deg 6.162 r_dihedral_angle_1_deg 6.043 r_scangle_other 5.286 r_mcangle_it 4.927 r_mcangle_other 4.926 r_scbond_it 3.234 r_scbond_other 3.234 r_mcbond_it 3.126 r_mcbond_other 3.125 r_angle_refined_deg 0.91 r_angle_other_deg 0.311 r_chiral_restr 0.04 r_bond_refined_d 0.003 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 4223 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement SCALA data scaling HKL-2000 data reduction MOLREP phasing