X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UB4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5289100mM Tris-HCl, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3347.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.1α = 90
b = 111.8β = 91.4
c = 93γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U1.0SSRFBL17U

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
125095.240587

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT1UB422039622211293.040.2510.248980.29072RANDOM43.655
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]
-0.610.28-0.220.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.227
r_dihedral_angle_4_deg21.628
r_dihedral_angle_3_deg19.06
r_dihedral_angle_1_deg7.019
r_scangle_it4.088
r_scbond_it2.809
r_angle_refined_deg1.962
r_mcangle_it1.796
r_mcbond_it1.047
r_chiral_restr0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.227
r_dihedral_angle_4_deg21.628
r_dihedral_angle_3_deg19.06
r_dihedral_angle_1_deg7.019
r_scangle_it4.088
r_scbond_it2.809
r_angle_refined_deg1.962
r_mcangle_it1.796
r_mcbond_it1.047
r_chiral_restr0.14
r_bond_refined_d0.024
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4137
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling