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Crystal Structure of Eukaryotic Oxoiron MagKatG2 at pH 8.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UT2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 15% PEG4000, 0.1 M sodium acetate, pH 4.6 (+ PAA soaking + pH 8.5 soaking)
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.53 α = 90 b = 109.54 β = 90 c = 132.15 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 2013-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9717 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.6 20 99.5 0.099 0.087 11.2 4.5 196582
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 99.3 0.73 2.4 4.6
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 3UT2 1.6 19.94 186717 9850 99.44 0.16597 0.16472 0.176 0.18992 0.1999 RANDOM 17.96
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] -0.06 -0.5 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.318 r_dihedral_angle_4_deg 15.296 r_dihedral_angle_3_deg 12.12 r_dihedral_angle_1_deg 5.332 r_angle_refined_deg 1.394 r_angle_other_deg 0.794 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.318 r_dihedral_angle_4_deg 15.296 r_dihedral_angle_3_deg 12.12 r_dihedral_angle_1_deg 5.332 r_angle_refined_deg 1.394 r_angle_other_deg 0.794 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11283 Nucleic Acid Atoms Solvent Atoms 1573 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing