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X-ray crystal structure of Y16515 in CBP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XXH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2 M Sodium citrate tribasic dihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% v/v 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.42 49.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.53 α = 90 b = 55.87 β = 90 c = 113.4 γ = 90
Symmetry Space Group I 2 2 2
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 2020-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97852 SSRF BL19U1
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 1.48 56.7 99.9 0.129 0.135 0.039 0.995 9.8 11.7 26100
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 1.48 1.51 100 1.086 1.135 0.327 0.872 11.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5XXH 1.48 50.17 24812 1275 99.74 0.19281 0.19154 0.21882 0.2441 RANDOM 27.914
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] -2.17 3.02 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.924 r_dihedral_angle_4_deg 20.585 r_dihedral_angle_3_deg 15.302 r_long_range_B_refined 5.674 r_long_range_B_other 5.602 r_dihedral_angle_1_deg 5.34 r_scangle_other 4.195 r_scbond_it 2.639 r_scbond_other 2.637 r_mcangle_it 2.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.924 r_dihedral_angle_4_deg 20.585 r_dihedral_angle_3_deg 15.302 r_long_range_B_refined 5.674 r_long_range_B_other 5.602 r_dihedral_angle_1_deg 5.34 r_scangle_other 4.195 r_scbond_it 2.639 r_scbond_other 2.637 r_mcangle_it 2.453 r_mcangle_other 2.452 r_mcbond_it 1.585 r_mcbond_other 1.578 r_angle_other_deg 1.546 r_angle_refined_deg 1.447 r_chiral_restr 0.066 r_bond_refined_d 0.012 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 956 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement Aimless data scaling iMOSFLM data reduction MOLREP phasing