2IVN

Structure of UP1 protein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.625% PEG 4000, 0.3M KCL, 0.1M SODIUM CITRATE PH5.6
Crystal Properties
Matthews coefficientSolvent content
2.1441.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.933α = 90
b = 69.868β = 90
c = 75.723γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.652099.20.0625.14.1418532
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.691000.512.82.84

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 DIFFRACTIONMADTHROUGHOUT1.652037910198799.20.2130.2120.224RANDOM21.33
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]
0.79-0.51-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.707
r_dihedral_angle_4_deg19.749
r_dihedral_angle_3_deg11.397
r_dihedral_angle_1_deg4.734
r_scangle_it1.411
r_angle_refined_deg0.987
r_scbond_it0.86
r_mcangle_it0.518
r_mcbond_it0.308
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.707
r_dihedral_angle_4_deg19.749
r_dihedral_angle_3_deg11.397
r_dihedral_angle_1_deg4.734
r_scangle_it1.411
r_angle_refined_deg0.987
r_scbond_it0.86
r_mcangle_it0.518
r_mcbond_it0.308
r_nbtor_refined0.294
r_nbd_refined0.165
r_symmetry_vdw_refined0.101
r_xyhbond_nbd_refined0.078
r_symmetry_hbond_refined0.076
r_chiral_restr0.057
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2499
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling