5U57

Psf4 in complex with Fe2+ and (S)-2-HPP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP28222% PEG 3,350 0.1 M Ammonium Citrate 10 mg/mL Psf4 Crystallized Anaerobically
Crystal Properties
Matthews coefficientSolvent content
2.3146.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.903α = 90
b = 111.471β = 90
c = 128.762γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)CC (Half)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
12.7384.281000.1020.99515.75.921630
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.7342.74397.60.7060.7862.26

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.7384.2819996105997.430.259710.256860.31106RANDOM59.619
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]
2.530.51-3.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.297
r_dihedral_angle_3_deg15.771
r_dihedral_angle_4_deg14.631
r_long_range_B_refined9.974
r_long_range_B_other9.948
r_scangle_other6.756
r_dihedral_angle_1_deg6.691
r_mcangle_it6.157
r_mcangle_other6.157
r_scbond_it4.169
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.297
r_dihedral_angle_3_deg15.771
r_dihedral_angle_4_deg14.631
r_long_range_B_refined9.974
r_long_range_B_other9.948
r_scangle_other6.756
r_dihedral_angle_1_deg6.691
r_mcangle_it6.157
r_mcangle_other6.157
r_scbond_it4.169
r_scbond_other4.168
r_mcbond_it3.94
r_mcbond_other3.938
r_angle_refined_deg1.447
r_angle_other_deg1.134
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.005
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5859
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing