2FCQ

X-ray Crystal Structure of a Chemically Synthesized Ubiquitin with a Cubic Space Group


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.75298by mixing 2 ul of ubiquitin solution (20 mg/ml) and 0.5 ul of crystallization buffer solution. The crystallization buffer was prepared by mixing 3ml of HEPES buffer (0.1M), 3ml of poly(ethylene glycol) 3350 (25%, w/v), and 0.2ml of 1M cadmium acetate, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8256.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.059α = 90
b = 105.059β = 90
c = 105.059γ = 90
Symmetry
Space GroupP 43 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MIRRORS2004-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0000APS17-ID

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
13.33099.60.07223.911.93300
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)
13.33.421000.663.212.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1YIW, CHAIN B3.320295829399.750.250.246170.241490.28563RANDOM85
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.629
r_dihedral_angle_3_deg17.007
r_dihedral_angle_4_deg9.22
r_dihedral_angle_1_deg6.63
r_angle_refined_deg1.313
r_angle_other_deg0.715
r_symmetry_vdw_refined0.268
r_metal_ion_refined0.257
r_nbd_refined0.24
r_symmetry_vdw_other0.221
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.629
r_dihedral_angle_3_deg17.007
r_dihedral_angle_4_deg9.22
r_dihedral_angle_1_deg6.63
r_angle_refined_deg1.313
r_angle_other_deg0.715
r_symmetry_vdw_refined0.268
r_metal_ion_refined0.257
r_nbd_refined0.24
r_symmetry_vdw_other0.221
r_nbd_other0.188
r_symmetry_hbond_refined0.188
r_xyhbond_nbd_refined0.158
r_nbtor_other0.08
r_chiral_restr0.067
r_bond_refined_d0.012
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1164
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing