X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UYS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5293100 mM Na-citrate, 25 mM (NH4)2SO4 and 7 % PEG 8000, pH 5.0
Crystal Properties
Matthews coefficientSolvent content
2.2946.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.135α = 90
b = 130.349β = 115.45
c = 53.177γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2016-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.000SPring-8BL26B2

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
125010015.33.841687
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)
122.0399.90.5962.23.7

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 REPLACEMENTTHROUGHOUT3UYS25039503203999.950.189960.187210.24155RANDOM36.415
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]
-0.010.1-2.571.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.203
r_dihedral_angle_4_deg19.852
r_dihedral_angle_3_deg13.951
r_long_range_B_refined6.663
r_long_range_B_other6.663
r_dihedral_angle_1_deg6.22
r_scangle_other4.87
r_mcangle_it3.962
r_mcangle_other3.961
r_scbond_it3.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.203
r_dihedral_angle_4_deg19.852
r_dihedral_angle_3_deg13.951
r_long_range_B_refined6.663
r_long_range_B_other6.663
r_dihedral_angle_1_deg6.22
r_scangle_other4.87
r_mcangle_it3.962
r_mcangle_other3.961
r_scbond_it3.117
r_scbond_other3.116
r_mcbond_it2.713
r_mcbond_other2.712
r_angle_refined_deg1.667
r_angle_other_deg0.966
r_chiral_restr0.095
r_bond_refined_d0.014
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4655
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
MOLREPphasing