6HPU

Crystal structure of human Pif1 helicase in complex with ADP-AlF4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HPH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP274MES, Ca-acetate, PEG 20K, PEG550 MME
Crystal Properties
Matthews coefficientSolvent content
5.5177.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 209.85α = 90
b = 209.85β = 90
c = 78.885γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.92819DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.96104.931000.08117.112.317663151.7
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)
13.964.061000.8570.8922.912.8

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 REPLACEMENTTHROUGHOUT6HPH3.9691.031660779498.750.178510.175270.25252RANDOM151.675
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]
-5.5-2.75-5.517.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.469
r_long_range_B_refined31.397
r_long_range_B_other31.394
r_dihedral_angle_3_deg22.319
r_mcangle_it21.394
r_mcangle_other21.393
r_scangle_other21.075
r_dihedral_angle_4_deg18.578
r_mcbond_it13.905
r_mcbond_other13.904
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.469
r_long_range_B_refined31.397
r_long_range_B_other31.394
r_dihedral_angle_3_deg22.319
r_mcangle_it21.394
r_mcangle_other21.393
r_scangle_other21.075
r_dihedral_angle_4_deg18.578
r_mcbond_it13.905
r_mcbond_other13.904
r_scbond_it13.59
r_scbond_other13.578
r_dihedral_angle_1_deg10.022
r_angle_refined_deg1.558
r_angle_other_deg0.827
r_chiral_restr0.066
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms6359
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing