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Copper binding protein from Laetisaria arvalis (LaX325)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IBI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 20 mM L-Na-Glutamate, 20 mM DL-Alanine (racemic), 20 mM Glycine, 20 mM DL-Lysine HCl (racemic), 20 mM DL-Serine (racemic)
100 mM MES monohydrate pH 6.5 / 100 mM imidazole pH 6.5
20% (w/v) PEG 500 MME and 10% (w/v) PEG 20.000.
Crystal Properties Matthews coefficient Solvent content 2.71 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.92 α = 90 b = 74.92 β = 90 c = 64.39 γ = 90
Symmetry Space Group P 43 21 2
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 EIGER X 16M Kirkpatrick-Baez (KB) mirror pair (VFM, HFM) 2018-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9799 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.1 60 99.9 0.087 0.999 12.25 7.2 11173 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 99.9 0.1703 0.803 1.49 7.44
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 6IBI 2.1 48.88 10600 575 99.85 0.19647 0.19351 0.2041 0.25618 0.258 RANDOM 54.919
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] 2.2 2.2 -4.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.247 r_dihedral_angle_4_deg 12.578 r_dihedral_angle_3_deg 12.387 r_long_range_B_other 8.203 r_long_range_B_refined 8.201 r_dihedral_angle_1_deg 7.232 r_scangle_other 6.714 r_mcangle_it 5.304 r_mcangle_other 5.302 r_scbond_it 4.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.247 r_dihedral_angle_4_deg 12.578 r_dihedral_angle_3_deg 12.387 r_long_range_B_other 8.203 r_long_range_B_refined 8.201 r_dihedral_angle_1_deg 7.232 r_scangle_other 6.714 r_mcangle_it 5.304 r_mcangle_other 5.302 r_scbond_it 4.654 r_scbond_other 4.65 r_mcbond_it 3.769 r_mcbond_other 3.767 r_angle_refined_deg 1.255 r_angle_other_deg 0.823 r_chiral_restr 0.054 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 1125 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing