X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I15 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527720% PEG 3350, 0.4 M sodium formate, 0.3 M guanidine, 0.1 M MES
Crystal Properties
Matthews coefficientSolvent content
2.754.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.72α = 90
b = 120.17β = 108.05
c = 68.17γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MCRL2015-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
12.279.9899.50.050.0620.0350.99810.12.843570
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)
12.22.3299.70.3640.4470.2560.9022.52.9

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 REPLACEMENTTHROUGHOUT4I152.279.9841186219199.060.19540.193030.23959RANDOM62.717
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]
6.60.32-1.78-4.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.772
r_dihedral_angle_4_deg19.392
r_dihedral_angle_3_deg16.37
r_long_range_B_other11.169
r_long_range_B_refined11.162
r_scangle_other8.297
r_mcangle_it7.871
r_mcangle_other7.87
r_scbond_it5.554
r_scbond_other5.553
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.772
r_dihedral_angle_4_deg19.392
r_dihedral_angle_3_deg16.37
r_long_range_B_other11.169
r_long_range_B_refined11.162
r_scangle_other8.297
r_mcangle_it7.871
r_mcangle_other7.87
r_scbond_it5.554
r_scbond_other5.553
r_dihedral_angle_1_deg5.52
r_mcbond_it5.431
r_mcbond_other5.418
r_angle_refined_deg1.612
r_angle_other_deg1.042
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms5260
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing