X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E5E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52910.2 M MgCl2, 5mM MnCl2, 0.1 M Tris pH 8.5, 30%(w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.3948.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.899α = 90
b = 73.899β = 90
c = 127.457γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.175099.80.1280.1330.0376.612.811511
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)
12.172.2598.30.8930.9520.3190.7638.11090

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 REPLACEMENTTHROUGHOUT4E5E2.17501092654999.780.202420.198720.28166RANDOM38.33
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]
-0.87-0.44-0.872.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.652
r_dihedral_angle_3_deg19.052
r_dihedral_angle_4_deg18.307
r_dihedral_angle_1_deg7.658
r_long_range_B_refined6.668
r_long_range_B_other6.627
r_scangle_other4.494
r_mcangle_it3.442
r_mcangle_other3.442
r_scbond_it2.772
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.652
r_dihedral_angle_3_deg19.052
r_dihedral_angle_4_deg18.307
r_dihedral_angle_1_deg7.658
r_long_range_B_refined6.668
r_long_range_B_other6.627
r_scangle_other4.494
r_mcangle_it3.442
r_mcangle_other3.442
r_scbond_it2.772
r_scbond_other2.765
r_mcbond_it2.151
r_mcbond_other2.145
r_angle_refined_deg2.108
r_angle_other_deg1.207
r_chiral_restr0.132
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1452
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing