X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5C0Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529520 mg/mL protein in water mixed 1:1 with 30% PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.2545.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.609α = 110.01
b = 51.739β = 93.09
c = 61.748γ = 91.88
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2013-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.07812APS21-ID-D

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
11.30157.88196.590.08115.35.3952019045513.53
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)
11.3011.33589.380.5042.64.2

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 REPLACEMENTTHROUGHOUT5C0Z1.30157.8890455474496.590.149490.148020.17771RANDOM19.317
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]
0.98-1.550.510.1-0.14-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.934
r_dihedral_angle_4_deg33.483
r_sphericity_free32.943
r_rigid_bond_restr17.959
r_dihedral_angle_3_deg12.594
r_sphericity_bonded10.853
r_dihedral_angle_1_deg6.418
r_long_range_B_refined2.987
r_long_range_B_other2.598
r_scangle_other2.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.934
r_dihedral_angle_4_deg33.483
r_sphericity_free32.943
r_rigid_bond_restr17.959
r_dihedral_angle_3_deg12.594
r_sphericity_bonded10.853
r_dihedral_angle_1_deg6.418
r_long_range_B_refined2.987
r_long_range_B_other2.598
r_scangle_other2.071
r_angle_other_deg1.941
r_angle_refined_deg1.884
r_scbond_it1.805
r_scbond_other1.802
r_mcangle_it1.793
r_mcangle_other1.792
r_mcbond_it1.401
r_mcbond_other1.392
r_chiral_restr0.131
r_gen_planes_other0.034
r_bond_refined_d0.018
r_gen_planes_refined0.017
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3236
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms211

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing