X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MZ2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M Tris pH 7.5, 5%PGA, 15%PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.4950.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.17α = 90
b = 219.11β = 90.19
c = 220.23γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173PIXELDECTRIS PILATUS3 6M2015-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.96863ESRFID29

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
11.849.1996.10.0926.582.3470418
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)
11.81.8594.90.6691.492.3

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 REPLACEMENTTHROUGHOUT5MZ21.849.194704182475996.10.1680.1670.192RANDOM27.7
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]
0.140.54-0.1-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.172
r_dihedral_angle_4_deg15.177
r_dihedral_angle_3_deg12.727
r_dihedral_angle_1_deg7.4
r_long_range_B_refined5.635
r_long_range_B_other5.525
r_angle_refined_deg1.564
r_angle_other_deg1.1
r_scangle_other0.883
r_mcangle_it0.768
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.172
r_dihedral_angle_4_deg15.177
r_dihedral_angle_3_deg12.727
r_dihedral_angle_1_deg7.4
r_long_range_B_refined5.635
r_long_range_B_other5.525
r_angle_refined_deg1.564
r_angle_other_deg1.1
r_scangle_other0.883
r_mcangle_it0.768
r_mcangle_other0.768
r_scbond_it0.55
r_scbond_other0.55
r_mcbond_it0.447
r_mcbond_other0.447
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.009
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 Atoms38218
Nucleic Acid Atoms
Solvent Atoms2940
Heterogen Atoms274

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata processing
XSCALEdata scaling
PHASERphasing
Omodel building