X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5G5YPDB ENTRY 5G5Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1820 % PEG6000, 0.1M SODIUM ACETATE PH 5.0, 0.02 M CALCIUM CHLORIDE
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.03α = 90
b = 129.74β = 96.34
c = 120.28γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2014-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I24DiamondI24

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
11.9957.3797.30.1257.13.61440382
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)
11.992.0477.20.8331.12.7

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 5G5Y1.99119.54136862712097.220.171830.169280.22092RANDOM29.493
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.826
r_dihedral_angle_4_deg19.299
r_dihedral_angle_3_deg13.783
r_dihedral_angle_1_deg6.932
r_mcangle_it3.041
r_scbond_it3.011
r_mcbond_it2.094
r_mcbond_other2.093
r_angle_refined_deg1.742
r_angle_other_deg1.018
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.826
r_dihedral_angle_4_deg19.299
r_dihedral_angle_3_deg13.783
r_dihedral_angle_1_deg6.932
r_mcangle_it3.041
r_scbond_it3.011
r_mcbond_it2.094
r_mcbond_other2.093
r_angle_refined_deg1.742
r_angle_other_deg1.018
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_refined0.008
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15685
Nucleic Acid Atoms
Solvent Atoms1650
Heterogen Atoms213

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing