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Bifunctional enzyme GlmU bound to Zn(II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HM8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 20 mM Tris-HCL, pH 7.2, 20% (v/v) PEG 400, 50 mM NaCl, 300 mM CaCl2, and 1 mM ZnCl2
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.872 α = 90 b = 92.872 β = 90 c = 280.703 γ = 120
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 2017-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.9 47 99.9 0.999 18.2 10.3 37206
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 0.943
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 1HM8 1.9 46.83 35343 1862 99.92 0.18721 0.18517 0.1938 0.22697 0.2362 RANDOM 39.347
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] 0.79 0.39 0.79 -2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.498 r_dihedral_angle_4_deg 23.503 r_dihedral_angle_3_deg 14.093 r_dihedral_angle_1_deg 7.015 r_long_range_B_refined 6.467 r_long_range_B_other 6.327 r_scangle_other 3.15 r_mcangle_it 2.448 r_mcangle_other 2.448 r_scbond_it 1.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.498 r_dihedral_angle_4_deg 23.503 r_dihedral_angle_3_deg 14.093 r_dihedral_angle_1_deg 7.015 r_long_range_B_refined 6.467 r_long_range_B_other 6.327 r_scangle_other 3.15 r_mcangle_it 2.448 r_mcangle_other 2.448 r_scbond_it 1.982 r_scbond_other 1.981 r_mcbond_it 1.586 r_mcbond_other 1.573 r_angle_refined_deg 1.551 r_angle_other_deg 1.289 r_chiral_restr 0.162 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 3354 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 60
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement