X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FGJPDB ENTRY 1FGJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH UNDER OIL7.529342% v/v PEG400, 50 mM potassium nitrate, 100 mM MES/NaOH, pH 7.5, MICROBATCH UNDER OIL, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7855.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.72α = 90
b = 141.97β = 90
c = 106.72γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6Mtwo horizontal deflecting and one vertical deflecting X-ray mirror2012-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P110.9786PETRA III, DESYP11

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
12.250.499.50.10213.65.69812498124
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)
12.22.399.30.588

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 1FGJ2.250.498124981241026399.970.182460.182460.179280.21273RANDOM29.017
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]
-2.150.261.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.164
r_dihedral_angle_4_deg17.906
r_dihedral_angle_3_deg14.63
r_dihedral_angle_1_deg5.055
r_scangle_it1.124
r_angle_refined_deg1.025
r_scbond_it0.723
r_mcangle_it0.536
r_mcbond_it0.283
r_chiral_restr0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.164
r_dihedral_angle_4_deg17.906
r_dihedral_angle_3_deg14.63
r_dihedral_angle_1_deg5.055
r_scangle_it1.124
r_angle_refined_deg1.025
r_scbond_it0.723
r_mcangle_it0.536
r_mcbond_it0.283
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_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 Atoms13309
Nucleic Acid Atoms
Solvent Atoms1094
Heterogen Atoms1038

Software

Software
Software NamePurpose
HEIDIdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling