X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Ammonium sulfate, MES
Crystal Properties
Matthews coefficientSolvent content
3.0259.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.123α = 90
b = 118.656β = 90
c = 124.504γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702015-05-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0000Photon FactoryAR-NE3A

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
125099.615.26.766057
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0598

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 REPLACEMENTTHROUGHOUT5GTF25062844321399.590.192990.190930.23327RANDOM30.189
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]
-0.040.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.747
r_dihedral_angle_4_deg21.794
r_dihedral_angle_3_deg16.093
r_long_range_B_refined8.311
r_long_range_B_other8.215
r_dihedral_angle_1_deg6.872
r_scangle_other5.77
r_scbond_it3.842
r_scbond_other3.841
r_mcangle_it3.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.747
r_dihedral_angle_4_deg21.794
r_dihedral_angle_3_deg16.093
r_long_range_B_refined8.311
r_long_range_B_other8.215
r_dihedral_angle_1_deg6.872
r_scangle_other5.77
r_scbond_it3.842
r_scbond_other3.841
r_mcangle_it3.095
r_mcangle_other3.095
r_mcbond_it2.308
r_mcbond_other2.299
r_angle_refined_deg1.852
r_angle_other_deg0.863
r_chiral_restr0.11
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4870
Nucleic Acid Atoms
Solvent Atoms352
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing