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High resolution Zn containing Iron sulfur cluster repair protein YtfE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FNN PDB ENTRY 5FNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.1 M TRIS/HCL PH 8.5 20% PEG8000 0.2 M MGCL2
Crystal Properties Matthews coefficient Solvent content 3.09 60.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.454 α = 90 b = 98.454 β = 90 c = 126.138 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 MIRRORS 2014-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 25.9 92.6 0.03 18.11 2.9 51147 -3
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 1.8 1.85 74 0.55 2.42 2.8
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 PDB ENTRY 5FNN 1.8 25.87 48586 2561 92.56 0.18728 0.18594 0.1936 0.2126 0.2192 RANDOM 44.525
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] 1.84 1.84 -3.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.031 r_dihedral_angle_4_deg 18.157 r_dihedral_angle_3_deg 12.712 r_dihedral_angle_1_deg 4.186 r_mcangle_it 2.659 r_scbond_it 2.577 r_mcbond_it 1.709 r_mcbond_other 1.709 r_angle_refined_deg 1.439 r_angle_other_deg 1.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.031 r_dihedral_angle_4_deg 18.157 r_dihedral_angle_3_deg 12.712 r_dihedral_angle_1_deg 4.186 r_mcangle_it 2.659 r_scbond_it 2.577 r_mcbond_it 1.709 r_mcbond_other 1.709 r_angle_refined_deg 1.439 r_angle_other_deg 1.174 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.003 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_mcangle_other 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 3282 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing