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Copper binding protein from Laetisaria arvalis (LaX325)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 MRC plates with 1:1 ratio drops (enzyme:reservoir solution) and 100 ul reservoir using an Oryx-8 robot.
Protein: 13.3 mg/ml in 20 mM MES pH 6.0.
Reservoir: 20 mM L-Na-Glutamate, 20 mM DL-Alanine (racemic), 20 mM Glycine, 20 mM DL-Lysine HCl (racemic), 20 mM DL-Serine (racemic), 50 mM MES monohydrate pH 6.5, 50 mM imidazole pH 6.5. 20% (w/v) PEG 500 MME and 10% (w/v) PEG 20000.
Crystal Properties Matthews coefficient Solvent content 3.42 64.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.599 α = 90 b = 84.635 β = 90 c = 127.319 γ = 90
Symmetry Space Group P 21 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 PILATUS 6M-F 2018-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.299 ESRF ID29
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 2.08 100 99.6 0.152 0.998 12.93 14 57268 -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 2.08 2.13 98.5 1.398 0.744 1.07 14.3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.08 42.35 52714 2641 99.53 0.2454 0.24417 0.2504 0.27087 0.275 RANDOM 43.444
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] 1.04 1.78 -2.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.884 r_dihedral_angle_3_deg 13.254 r_dihedral_angle_4_deg 11.447 r_long_range_B_other 8.353 r_long_range_B_refined 8.352 r_dihedral_angle_1_deg 6.698 r_scangle_other 6.226 r_mcangle_it 4.833 r_mcangle_other 4.832 r_scbond_it 4.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.884 r_dihedral_angle_3_deg 13.254 r_dihedral_angle_4_deg 11.447 r_long_range_B_other 8.353 r_long_range_B_refined 8.352 r_dihedral_angle_1_deg 6.698 r_scangle_other 6.226 r_mcangle_it 4.833 r_mcangle_other 4.832 r_scbond_it 4.237 r_scbond_other 4.237 r_mcbond_it 3.448 r_mcbond_other 3.446 r_angle_other_deg 2.412 r_angle_refined_deg 1.383 r_chiral_restr 0.063 r_gen_planes_other 0.047 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_bond_other_d 0.002 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 4569 Nucleic Acid Atoms Solvent Atoms 549 Heterogen Atoms 386
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XSCALE data scaling PHENIX phasing AutoSol phasing PHASER phasing Coot model building