X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.09 M HEPES, pH 7.5, 1.26 M Sodium Citrate, 10% v/v glycerol
Crystal Properties
Matthews coefficientSolvent content
2.8556.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.284α = 90
b = 70.284β = 90
c = 448.355γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002016-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.9787APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.785099.50.97634.26.1235628
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.841000.87326.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.7838.581971191037787.640.155910.15460.18098RANDOM25.989
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]
-0.24-0.12-0.240.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.064
r_dihedral_angle_3_deg14.14
r_dihedral_angle_4_deg13.747
r_long_range_B_other8.684
r_long_range_B_refined8.683
r_scangle_other7.261
r_dihedral_angle_1_deg6.492
r_scbond_other5.861
r_scbond_it5.86
r_mcangle_it3.261
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.064
r_dihedral_angle_3_deg14.14
r_dihedral_angle_4_deg13.747
r_long_range_B_other8.684
r_long_range_B_refined8.683
r_scangle_other7.261
r_dihedral_angle_1_deg6.492
r_scbond_other5.861
r_scbond_it5.86
r_mcangle_it3.261
r_mcangle_other3.261
r_mcbond_it2.565
r_mcbond_other2.565
r_angle_refined_deg1.329
r_angle_other_deg1.324
r_chiral_restr0.068
r_gen_planes_refined0.017
r_gen_planes_other0.01
r_bond_refined_d0.006
r_bond_other_d
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 Atoms15060
Nucleic Acid Atoms
Solvent Atoms1501
Heterogen Atoms310

Software

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