5FNY

Low solvent content crystal form of Zn containing Iron sulfur cluster repair protein YtfE


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
190.1M BICINE PH9.0, 2.4M AMMONIUM REMARK 280 SULFATE, 2% PEG400
Crystal Properties
Matthews coefficientSolvent content
2.0640.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.024α = 90
b = 86.495β = 90
c = 51.159γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2014-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B1NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0125.293.40.0418.113.926225-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.012.0675.20.532.422.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 5FNN2.0125.1724951127493.450.190940.188740.23476RANDOM39.124
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]
-2.521.131.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.289
r_dihedral_angle_4_deg25.524
r_dihedral_angle_3_deg13.529
r_dihedral_angle_1_deg4.675
r_mcangle_it2.092
r_scbond_it1.923
r_angle_refined_deg1.441
r_mcbond_it1.31
r_mcbond_other1.309
r_angle_other_deg1.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.289
r_dihedral_angle_4_deg25.524
r_dihedral_angle_3_deg13.529
r_dihedral_angle_1_deg4.675
r_mcangle_it2.092
r_scbond_it1.923
r_angle_refined_deg1.441
r_mcbond_it1.31
r_mcbond_other1.309
r_angle_other_deg1.155
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.004
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 AtomsNumber
Protein Atoms3289
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing