X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Y8E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.22776-11% iso-propanol, 0.1 M Mes pH 6.5, 0.1 M sodium acetate pH 4.5 and 0.2 M calcium acetate.
Crystal Properties
Matthews coefficientSolvent content
2.4148.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.23α = 90
b = 59.4β = 115.03
c = 92.78γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9200DiamondI04-1

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
12.4484.0798.050.05717.34.52040519345
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)
12.442.50398.810.94524.8

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 REPLACEMENTTHROUGHOUT4Y8E2.4484.0719345106098.050.190940.187950.24651RANDOM72.026
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]
-0.64-0.340.40.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.225
r_dihedral_angle_4_deg20.168
r_dihedral_angle_3_deg17.627
r_long_range_B_refined13.209
r_long_range_B_other13.208
r_scangle_other10.152
r_dihedral_angle_1_deg7.869
r_mcangle_other7.82
r_mcangle_it7.819
r_scbond_it7.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.225
r_dihedral_angle_4_deg20.168
r_dihedral_angle_3_deg17.627
r_long_range_B_refined13.209
r_long_range_B_other13.208
r_scangle_other10.152
r_dihedral_angle_1_deg7.869
r_mcangle_other7.82
r_mcangle_it7.819
r_scbond_it7.136
r_scbond_other7.125
r_mcbond_it5.773
r_mcbond_other5.754
r_angle_refined_deg1.999
r_angle_other_deg1.509
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.008
r_gen_planes_other0.006
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 Atoms3931
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing