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Crystal structure of Cph001-D189N
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7F0A
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 2.57 52.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.299 α = 90 b = 86.937 β = 90 c = 87.015 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 2022-06-02 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 2.3 30 99.9 0.057 28.99 5.5 28419
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 2.3 2.38 100 0.582 0.969 3.429 5.6
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 2.3 28.28 26244 1390 97.14 0.19712 0.19441 0.2008 0.24504 0.2471 RANDOM 34.244
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] -0.04 0.07 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.504 r_dihedral_angle_1_deg 6.387 r_long_range_B_refined 6.347 r_long_range_B_other 6.344 r_dihedral_angle_2_deg 4.997 r_scangle_other 4.238 r_mcangle_it 3.784 r_mcangle_other 3.784 r_scbond_it 2.551 r_scbond_other 2.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.504 r_dihedral_angle_1_deg 6.387 r_long_range_B_refined 6.347 r_long_range_B_other 6.344 r_dihedral_angle_2_deg 4.997 r_scangle_other 4.238 r_mcangle_it 3.784 r_mcangle_other 3.784 r_scbond_it 2.551 r_scbond_other 2.551 r_mcbond_it 2.301 r_mcbond_other 2.295 r_angle_refined_deg 1.127 r_angle_other_deg 0.388 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 4209 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling MOLREP phasing