X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4KEYpdb entry 4KEY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277200mM MgCl2, 20% PEG 3500, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7955.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.42α = 90
b = 132.88β = 90
c = 147.49γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.836699.96.610299010299026
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)
11.831.8899.80.6192.55.87523

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 4KEY1.83669775497754514799.910.187860.187860.18610.2214RANDOM22.325
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]
-0.170.33-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.077
r_dihedral_angle_4_deg18.908
r_dihedral_angle_3_deg14.006
r_dihedral_angle_1_deg6.648
r_scangle_it4.976
r_scbond_it3.206
r_mcangle_it2.117
r_angle_refined_deg1.935
r_mcbond_it1.255
r_angle_other_deg1.059
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.077
r_dihedral_angle_4_deg18.908
r_dihedral_angle_3_deg14.006
r_dihedral_angle_1_deg6.648
r_scangle_it4.976
r_scbond_it3.206
r_mcangle_it2.117
r_angle_refined_deg1.935
r_mcbond_it1.255
r_angle_other_deg1.059
r_mcbond_other0.38
r_chiral_restr0.126
r_bond_refined_d0.025
r_gen_planes_refined0.011
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_mcangle_other
r_scbond_other
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 Atoms7206
Nucleic Acid Atoms
Solvent Atoms569
Heterogen Atoms132

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling