5MLO | pdb_00005mlo

Crystal structure of human PCNA in complex with ZRANB3 PIP box peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VYM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293100 mM NaCl + 8% (v/v) DMSO + 31% pentaerythitol propoxylate (5/4 PO/OH)
Crystal Properties
Matthews coefficientSolvent content
2.5251.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.136α = 90
b = 86.802β = 90
c = 156.679γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I041.1402DiamondI04

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
11.9678.341000.0840.99920.21367566
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)
11.962.011001.7630.5661.513

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1VYM1.9678.3464155332599.950.213630.211290.220.259330.26RANDOM44.945
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]
-0.27-2.222.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.647
r_dihedral_angle_4_deg16.818
r_dihedral_angle_3_deg15.252
r_long_range_B_refined8.498
r_long_range_B_other8.404
r_dihedral_angle_1_deg7.255
r_scangle_other4.617
r_mcangle_it3.904
r_mcangle_other3.904
r_scbond_it2.855
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.647
r_dihedral_angle_4_deg16.818
r_dihedral_angle_3_deg15.252
r_long_range_B_refined8.498
r_long_range_B_other8.404
r_dihedral_angle_1_deg7.255
r_scangle_other4.617
r_mcangle_it3.904
r_mcangle_other3.904
r_scbond_it2.855
r_scbond_other2.855
r_mcbond_it2.452
r_mcbond_other2.45
r_angle_refined_deg1.401
r_angle_other_deg1.091
r_chiral_restr0.097
r_gen_planes_refined0.012
r_bond_refined_d0.01
r_gen_planes_other0.007
r_bond_other_d0.005
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 Atoms6175
Nucleic Acid Atoms
Solvent Atoms385
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing