5FNP

High resolution Zn containing Iron sulfur cluster repair protein YtfE


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.1 M TRIS/HCL PH 8.5 20% PEG8000 0.2 M MGCL2
Crystal Properties
Matthews coefficientSolvent content
3.0960.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.454α = 90
b = 98.454β = 90
c = 126.138γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2014-04-29MSINGLE 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
11.825.992.60.0318.112.951147-3
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)
11.81.85740.552.422.8

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 5FNN1.825.8748586256192.560.187280.185940.2126RANDOM44.525
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]
1.841.84-3.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.031
r_dihedral_angle_4_deg18.157
r_dihedral_angle_3_deg12.712
r_dihedral_angle_1_deg4.186
r_mcangle_it2.659
r_scbond_it2.577
r_mcbond_it1.709
r_mcbond_other1.709
r_angle_refined_deg1.439
r_angle_other_deg1.174
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.031
r_dihedral_angle_4_deg18.157
r_dihedral_angle_3_deg12.712
r_dihedral_angle_1_deg4.186
r_mcangle_it2.659
r_scbond_it2.577
r_mcbond_it1.709
r_mcbond_other1.709
r_angle_refined_deg1.439
r_angle_other_deg1.174
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.003
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 AtomsNumber
Protein Atoms3282
Nucleic Acid Atoms
Solvent Atoms438
Heterogen Atoms8

Software

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