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The X183 domain from Cellvibrio japonicus Cbp2D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES pH 7.5, 20% w/v PEG 4000, 10% w/v propan-2-ol
Crystal Properties Matthews coefficient Solvent content 2.07 40.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.509 α = 90 b = 55.376 β = 90 c = 55.855 γ = 90
Symmetry Space Group P 2 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 PIXEL DECTRIS PILATUS3 6M 2018-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 1.2 55.85 100 0.05 0.06 0.033 0.997 48.3 6 28435
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 1.2 1.22 0.088 0.105 0.057 0.99 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.2 39.356 28390 1404 99.923 0.113 0.1124 0.1125 0.1279 0.128 11.724
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] -0.098 0.262 -0.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.673 r_dihedral_angle_4_deg 21.522 r_dihedral_angle_other_3_deg 16.384 r_dihedral_angle_3_deg 9.989 r_mcbond_it 9.275 r_mcbond_other 9.274 r_rigid_bond_restr 8.942 r_mcangle_it 8.121 r_mcangle_other 8.117 r_dihedral_angle_1_deg 6.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.673 r_dihedral_angle_4_deg 21.522 r_dihedral_angle_other_3_deg 16.384 r_dihedral_angle_3_deg 9.989 r_mcbond_it 9.275 r_mcbond_other 9.274 r_rigid_bond_restr 8.942 r_mcangle_it 8.121 r_mcangle_other 8.117 r_dihedral_angle_1_deg 6.215 r_lrange_it 5.995 r_lrange_other 5.995 r_scangle_it 2.484 r_scangle_other 2.482 r_scbond_it 2.073 r_scbond_other 2.073 r_angle_refined_deg 1.945 r_angle_other_deg 1.852 r_symmetry_xyhbond_nbd_refined 0.308 r_nbd_refined 0.263 r_symmetry_nbd_refined 0.252 r_nbd_other 0.207 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.18 r_metal_ion_refined 0.117 r_chiral_restr 0.114 r_xyhbond_nbd_refined 0.098 r_symmetry_nbtor_other 0.092 r_gen_planes_other 0.026 r_bond_refined_d 0.022 r_gen_planes_refined 0.021 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 715 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data reduction Aimless data scaling SHELXDE phasing