6J2Z

AtFKBP53 N-terminal Nucleoplasmin Domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K5J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72910.2 M DL-Malic acid (pH 7.0), 25% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3843.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.59α = 90
b = 97.39β = 94.12
c = 96.43γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9537ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.468.531000.0630.0730.0290.99916.56.64083756.493
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.491000.5090.6090.240.9053.26.5

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 REPLACEMENTTHROUGHOUT1K5J2.468.5338867203399.990.205380.2040.23325RANDOM69
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]
-1.33-2.250.471.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.38
r_dihedral_angle_3_deg14.903
r_dihedral_angle_4_deg12.11
r_dihedral_angle_1_deg8.051
r_long_range_B_refined7.038
r_long_range_B_other7.037
r_scangle_other4.877
r_mcangle_it4.074
r_mcangle_other4.073
r_scbond_it3.265
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.38
r_dihedral_angle_3_deg14.903
r_dihedral_angle_4_deg12.11
r_dihedral_angle_1_deg8.051
r_long_range_B_refined7.038
r_long_range_B_other7.037
r_scangle_other4.877
r_mcangle_it4.074
r_mcangle_other4.073
r_scbond_it3.265
r_scbond_other3.265
r_mcbond_it2.72
r_mcbond_other2.719
r_angle_refined_deg1.527
r_angle_other_deg1.182
r_chiral_restr0.131
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.001
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 Atoms7179
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing