X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XLL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.1291.1514% (w/v) PEG 3350, 0.1 M succinic acid, protein concentration 25 mg/ml
Crystal Properties
Matthews coefficientSolvent content
3.2562.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.382α = 90
b = 203.846β = 90
c = 226.744γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.5947.31000.1440.1570.0610.99413.56.548305-3.730.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.592.6799.90.8580.9630.4280.60824.9

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 REPLACEMENTTHROUGHOUT2XLL2.5947.348305244299.890.16180.16010.2257random selection36.142
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]
-0.47-1.722.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.954
r_dihedral_angle_4_deg19.554
r_dihedral_angle_3_deg14.747
r_dihedral_angle_1_deg7.627
r_long_range_B_refined6.017
r_long_range_B_other6.004
r_scangle_other4.194
r_mcangle_other3.421
r_mcangle_it3.42
r_scbond_it2.808
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.954
r_dihedral_angle_4_deg19.554
r_dihedral_angle_3_deg14.747
r_dihedral_angle_1_deg7.627
r_long_range_B_refined6.017
r_long_range_B_other6.004
r_scangle_other4.194
r_mcangle_other3.421
r_mcangle_it3.42
r_scbond_it2.808
r_scbond_other2.808
r_mcbond_it2.162
r_mcbond_other2.159
r_angle_refined_deg1.35
r_angle_other_deg0.819
r_chiral_restr0.059
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8476
Nucleic Acid Atoms
Solvent Atoms547
Heterogen Atoms357

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing