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Structure of YfiY from Bacillus cereus bound to the siderophore iron (III) schizokinen
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 312 Protein 10-20 mg/ml, 0.1M HEPES 7.0, 30% Jeffamine ED-2001. Direct cryoprotection. , VAPOR DIFFUSION, HANGING DROP, temperature 312K
Crystal Properties Matthews coefficient Solvent content 2.69 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.796 α = 90 b = 47.328 β = 112.88 c = 64.981 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315 2010-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97 ALS 5.0.2
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 1.55 50 99.5 0.118 9.2 7.3 46458
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.61
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.55 50 44098 2344 98.32 0.1731 0.1723 0.1808 0.1891 0.197 RANDOM 21.1498
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] 0.01 -0.13 0.51 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.512 r_dihedral_angle_4_deg 20.361 r_dihedral_angle_3_deg 11.84 r_dihedral_angle_1_deg 5.488 r_scangle_it 2.48 r_scbond_it 1.465 r_angle_refined_deg 1.109 r_mcangle_it 0.86 r_angle_other_deg 0.823 r_mcbond_it 0.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.512 r_dihedral_angle_4_deg 20.361 r_dihedral_angle_3_deg 11.84 r_dihedral_angle_1_deg 5.488 r_scangle_it 2.48 r_scbond_it 1.465 r_angle_refined_deg 1.109 r_mcangle_it 0.86 r_angle_other_deg 0.823 r_mcbond_it 0.437 r_mcbond_other 0.076 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2170 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling