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Low solvent content crystal form of 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 9 0.1M BICINE PH9.0, 2.4M AMMONIUM REMARK 280 SULFATE, 2% PEG400
Crystal Properties Matthews coefficient Solvent content 2.06 40.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.024 α = 90 b = 86.495 β = 90 c = 51.159 γ = 90
Symmetry Space Group P 21 21 2
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 2014-06-28 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 2.01 25.2 93.4 0.04 18.11 3.9 26225 -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 2.01 2.06 75.2 0.53 2.42 2.3
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 2.01 25.17 24951 1274 93.45 0.19094 0.18874 0.195 0.23476 0.2424 RANDOM 39.124
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] -2.52 1.13 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.289 r_dihedral_angle_4_deg 25.524 r_dihedral_angle_3_deg 13.529 r_dihedral_angle_1_deg 4.675 r_mcangle_it 2.092 r_scbond_it 1.923 r_angle_refined_deg 1.441 r_mcbond_it 1.31 r_mcbond_other 1.309 r_angle_other_deg 1.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.289 r_dihedral_angle_4_deg 25.524 r_dihedral_angle_3_deg 13.529 r_dihedral_angle_1_deg 4.675 r_mcangle_it 2.092 r_scbond_it 1.923 r_angle_refined_deg 1.441 r_mcbond_it 1.31 r_mcbond_other 1.309 r_angle_other_deg 1.155 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 3289 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing