4KDC

Crystal Structure of UBIG


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52870.1M HEPES pH7.5 and 20% polyethylene glycol 10000, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
2.4850.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.848α = 90
b = 58.584β = 105.26
c = 40.168γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287IMAGE PLATEMAR scanner 345 mm plate2010-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R0.9994

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.0929.51

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.0929.511477477797.330.184820.182710.22459RANDOM28.188
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]
1.65-0.98-0.03-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.144
r_dihedral_angle_4_deg18.726
r_dihedral_angle_3_deg13.976
r_dihedral_angle_1_deg5.667
r_angle_other_deg3.648
r_mcangle_it2.434
r_scbond_it2.098
r_mcbond_it1.531
r_mcbond_other1.531
r_angle_refined_deg1.232
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.144
r_dihedral_angle_4_deg18.726
r_dihedral_angle_3_deg13.976
r_dihedral_angle_1_deg5.667
r_angle_other_deg3.648
r_mcangle_it2.434
r_scbond_it2.098
r_mcbond_it1.531
r_mcbond_other1.531
r_angle_refined_deg1.232
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_other0.006
r_gen_planes_refined0.004
r_bond_other_d
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms1643
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling