X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UBQPDB ENTRY 1UBQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.9279.1527-32% PEG 4000, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K
Crystal Properties
Matthews coefficientSolvent content
1.73655429.170057

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 27.124α = 90
b = 53.035β = 90
c = 87.268γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-1180 cm lens focused ccd2004-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.12711ALS4.2.2

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
11.3533.69197.80.06810.84.982849927867
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)
1.351.490.690.60.5032.44.372511

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 1UBQ1.3533.6912849927864140597.780.189980.189980.188050.22589RANDOM33.353
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]
-0.590.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.53
r_dihedral_angle_4_deg20.878
r_dihedral_angle_3_deg13.379
r_dihedral_angle_1_deg6.042
r_scangle_it4.494
r_scbond_it3.215
r_sphericity_bonded2.737
r_mcangle_it1.946
r_rigid_bond_restr1.921
r_mcbond_it1.657
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.53
r_dihedral_angle_4_deg20.878
r_dihedral_angle_3_deg13.379
r_dihedral_angle_1_deg6.042
r_scangle_it4.494
r_scbond_it3.215
r_sphericity_bonded2.737
r_mcangle_it1.946
r_rigid_bond_restr1.921
r_mcbond_it1.657
r_angle_refined_deg1.416
r_angle_other_deg0.86
r_mcbond_other0.646
r_symmetry_vdw_other0.243
r_symmetry_vdw_refined0.207
r_nbd_refined0.206
r_nbd_other0.188
r_nbtor_refined0.165
r_xyhbond_nbd_refined0.165
r_symmetry_hbond_refined0.147
r_chiral_restr0.083
r_nbtor_other0.08
r_xyhbond_nbd_other0.04
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1259
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms

Software

Software
Software NamePurpose
d*TREKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection