6HPH

Crystal structure of human Pif1 helicase in complex with AMP-PNP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277Na-acetate, PEG 8K, PEG1K
Crystal Properties
Matthews coefficientSolvent content
2.2445.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.28α = 90
b = 143.29β = 90
c = 77.64γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152015-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

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
11.1349.9598.70.0680.99711.26.314992721.1
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)
11.131.1689.630.80.8961.44

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 REPLACEMENTTHROUGHOUT6HPQ1.1349.95142572730798.540.128810.127010.16304RANDOM21.133
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]
0.120.91-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free44.717
r_dihedral_angle_2_deg36.317
r_dihedral_angle_4_deg22.121
r_sphericity_bonded15.715
r_dihedral_angle_3_deg14.198
r_long_range_B_refined7.005
r_rigid_bond_restr6.577
r_dihedral_angle_1_deg5.966
r_long_range_B_other5.888
r_scangle_other5.771
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free44.717
r_dihedral_angle_2_deg36.317
r_dihedral_angle_4_deg22.121
r_sphericity_bonded15.715
r_dihedral_angle_3_deg14.198
r_long_range_B_refined7.005
r_rigid_bond_restr6.577
r_dihedral_angle_1_deg5.966
r_long_range_B_other5.888
r_scangle_other5.771
r_scbond_it4.503
r_scbond_other4.502
r_mcangle_other3.044
r_mcangle_it3.032
r_angle_refined_deg2.496
r_mcbond_it2.453
r_mcbond_other2.424
r_angle_other_deg1.604
r_chiral_restr0.165
r_bond_refined_d0.029
r_gen_planes_refined0.013
r_gen_planes_other0.008
r_bond_other_d0.003
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3187
Nucleic Acid Atoms
Solvent Atoms857
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
SCALEPACKdata scaling
MOLREPphasing