X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M Ammonium nitrate, 34% (w/v) PEG 3350, 0.01 M copper (II) chloride dihydrate, 2 mM TCEP, 10 mM TH588, 6 mM MgCL2.
Crystal Properties
Matthews coefficientSolvent content
2.957.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.673α = 90
b = 142.088β = 107.52
c = 58.75γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.447.4990.2710.98153.935400
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4995.41.4450.4291.13.8

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 REPLACEMENTTHROUGHOUT5MZG2.447.433560181198.930.251180.248610.29924RANDOM27.34
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]
-0.58-0.31.25-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.18
r_dihedral_angle_3_deg13.045
r_dihedral_angle_4_deg12.711
r_dihedral_angle_1_deg5.726
r_long_range_B_refined2.644
r_long_range_B_other2.644
r_mcangle_it1.221
r_mcangle_other1.221
r_angle_refined_deg1.06
r_angle_other_deg0.805
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.18
r_dihedral_angle_3_deg13.045
r_dihedral_angle_4_deg12.711
r_dihedral_angle_1_deg5.726
r_long_range_B_refined2.644
r_long_range_B_other2.644
r_mcangle_it1.221
r_mcangle_other1.221
r_angle_refined_deg1.06
r_angle_other_deg0.805
r_scangle_other0.796
r_mcbond_it0.663
r_mcbond_other0.663
r_scbond_it0.429
r_scbond_other0.429
r_chiral_restr0.065
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.001
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 Atoms4966
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms216

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing