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X-ray structure of a zinc binding GB1 mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IGD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 291 70% MPD, 200 mM ZnSO4, 50 mM NaCI, pH 4.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.178 α = 90 b = 54.178 β = 90 c = 81.077 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 PILATUS 2M-F 2016-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.9 46.92 99.9 0.086 17.2 10.6 120455 11371
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 92.8 0.838 2.6 10.5 1631
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 1IGD 1.9 46.92 10822 521 99.92 0.20779 0.2065 0.2178 0.23392 0.2453 RANDOM 49.62
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] 1.82 0.91 1.82 -5.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.619 r_dihedral_angle_3_deg 13.294 r_long_range_B_refined 8.816 r_long_range_B_other 8.816 r_dihedral_angle_1_deg 7.476 r_scangle_other 5.793 r_mcangle_it 3.894 r_mcangle_other 3.892 r_scbond_it 3.636 r_scbond_other 3.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.619 r_dihedral_angle_3_deg 13.294 r_long_range_B_refined 8.816 r_long_range_B_other 8.816 r_dihedral_angle_1_deg 7.476 r_scangle_other 5.793 r_mcangle_it 3.894 r_mcangle_other 3.892 r_scbond_it 3.636 r_scbond_other 3.628 r_mcbond_it 2.816 r_mcbond_other 2.797 r_angle_refined_deg 1.161 r_angle_other_deg 0.729 r_chiral_restr 0.09 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_4_deg 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 450 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing