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Ang-1 domain of the HupE/UreJ-2 protein from Rhodobacteraceae bacterium RbAng-1a with Cu bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Zn sulfate, MES, polyethylene glycol monomethyl ether 550.
Crystal Properties Matthews coefficient Solvent content 3.28 62.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.593 α = 90 b = 79.593 β = 90 c = 63.453 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 100 PIXEL DECTRIS EIGER2 XE 16M 2023-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 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 2.25 46.68 100 0.136 0.144 0.046 0.995 12.8 17.7 11371
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) 2.25 2.32 100 1.626 1.732 0.593 0.618 2 16.2
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.25 46.68 11350 554 99.991 0.218 0.2158 0.2158 0.2554 0.2556 60.702
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] 1.609 0.804 1.609 -5.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.385 r_dihedral_angle_3_deg 12.193 r_lrange_other 9.037 r_lrange_it 9.031 r_scangle_it 8.484 r_scangle_other 8.479 r_dihedral_angle_1_deg 8.187 r_dihedral_angle_2_deg 7.903 r_scbond_it 7.085 r_scbond_other 7.045
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.385 r_dihedral_angle_3_deg 12.193 r_lrange_other 9.037 r_lrange_it 9.031 r_scangle_it 8.484 r_scangle_other 8.479 r_dihedral_angle_1_deg 8.187 r_dihedral_angle_2_deg 7.903 r_scbond_it 7.085 r_scbond_other 7.045 r_mcangle_it 6.834 r_mcangle_other 6.831 r_mcbond_it 5.725 r_mcbond_other 5.721 r_angle_refined_deg 2.371 r_angle_other_deg 1.093 r_symmetry_nbd_refined 0.265 r_symmetry_xyhbond_nbd_refined 0.184 r_nbd_refined 0.178 r_xyhbond_nbd_refined 0.156 r_symmetry_nbd_other 0.145 r_nbtor_refined 0.136 r_nbd_other 0.117 r_chiral_restr 0.114 r_symmetry_metal_ion_refined 0.094 r_symmetry_nbtor_other 0.072 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1204 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction XSCALE data scaling Aimless data scaling PHASER phasing