1X23

Crystal structure of ubch5c


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52880.1M HEPES-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
238.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.998α = 90
b = 44.334β = 93.36
c = 97.584γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-60402004-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.900SPring-8BL44XU

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
11.810093.90.0420.92.84607721.7
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)
1.81.8683.80.249

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QCQ1.85204607741012217894.680.203760.203760.199490.28222RANDOM28.5
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]
0.610.57-0.550.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.404
r_dihedral_angle_4_deg17.452
r_dihedral_angle_3_deg17.039
r_dihedral_angle_1_deg6.089
r_scangle_it3.763
r_scbond_it2.538
r_mcangle_it1.611
r_angle_refined_deg1.467
r_mcbond_it0.993
r_nbtor_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.404
r_dihedral_angle_4_deg17.452
r_dihedral_angle_3_deg17.039
r_dihedral_angle_1_deg6.089
r_scangle_it3.763
r_scbond_it2.538
r_mcangle_it1.611
r_angle_refined_deg1.467
r_mcbond_it0.993
r_nbtor_refined0.321
r_xyhbond_nbd_refined0.247
r_nbd_refined0.24
r_symmetry_vdw_refined0.225
r_symmetry_hbond_refined0.18
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4867
Nucleic Acid Atoms
Solvent Atoms677
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing