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Crystal Structure Analysis of the CBP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 30% PEG 3350, 0.2M MgCl2, 0.1M Tris HCl, PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.16 43.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.32 α = 90 b = 44.32 β = 90 c = 121.292 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2016-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97791 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.62 60.65 100 0.085 0.088 0.021 0.998 22.2 17.4 18496
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.64 100 0.335 0.344 0.08 0.985 18.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4NYX 1.62 40.43 17589 859 100 0.192 0.191 0.2009 0.208 0.2194 RANDOM 17.71
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] 0.07 0.04 0.07 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.929 r_dihedral_angle_4_deg 14.264 r_dihedral_angle_3_deg 13.128 r_dihedral_angle_1_deg 5.156 r_angle_refined_deg 1.33 r_angle_other_deg 0.957 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.929 r_dihedral_angle_4_deg 14.264 r_dihedral_angle_3_deg 13.128 r_dihedral_angle_1_deg 5.156 r_angle_refined_deg 1.33 r_angle_other_deg 0.957 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 973 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing