X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YETPDB ENTRY 2YET

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.525% PEG3350, 0.1M BISTRIS PH 5.5, 0.2 M AMMONIUM ACETATE AS RESERVOIR. AFTERWARDS THE CRYSTAL WAS SOAKED IN A SOLUTION CONSISTING OF RESERVOIR TO WHICH CU(NO3)2 HAD BEEN ADDED TO A FINAL CONCENTRATION OF 10 MM
Crystal Properties
Matthews coefficientSolvent content
2.2344.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.5α = 90
b = 87.3β = 104.7
c = 37.3γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH SX-165MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL2011-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-2MAX III911-2

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
11.253093.20.0422.32.51065353
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)
11.251.2883.20.1461.82

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2YET1.2527.815306627931000.15630.155110.17925RANDOM18.293
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]
-0.450.17-0.070.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.079
r_dihedral_angle_3_deg11.854
r_dihedral_angle_4_deg8.443
r_dihedral_angle_1_deg6.244
r_scangle_it2.695
r_scbond_it1.898
r_mcangle_it1.388
r_angle_refined_deg1.327
r_mcbond_it0.858
r_rigid_bond_restr0.518
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.079
r_dihedral_angle_3_deg11.854
r_dihedral_angle_4_deg8.443
r_dihedral_angle_1_deg6.244
r_scangle_it2.695
r_scbond_it1.898
r_mcangle_it1.388
r_angle_refined_deg1.327
r_mcbond_it0.858
r_rigid_bond_restr0.518
r_chiral_restr0.091
r_bond_refined_d0.009
r_gen_planes_refined0.007
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1724
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing