X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2MGJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92982.64 M ammonium sulfate, 100 mM Tris-Cl, 1 mM EDTA
Crystal Properties
Matthews coefficientSolvent content
3.0759.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.15α = 90
b = 90.15β = 90
c = 45.324γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2017-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)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
11.64178.071000.120.05454.720847
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.6411.6841537

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 REPLACEMENTTHROUGHOUT2MGJ1.6478.071988795980.470.166690.165430.19325RANDOM17.575
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]
-0.05-0.02-0.050.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.755
r_dihedral_angle_4_deg19.473
r_dihedral_angle_3_deg13.658
r_long_range_B_refined5.752
r_long_range_B_other5.752
r_dihedral_angle_1_deg5.196
r_scangle_other4.179
r_scbond_it3.518
r_scbond_other2.903
r_mcangle_other2.194
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.755
r_dihedral_angle_4_deg19.473
r_dihedral_angle_3_deg13.658
r_long_range_B_refined5.752
r_long_range_B_other5.752
r_dihedral_angle_1_deg5.196
r_scangle_other4.179
r_scbond_it3.518
r_scbond_other2.903
r_mcangle_other2.194
r_mcangle_it2.185
r_angle_refined_deg2.142
r_mcbond_it1.513
r_mcbond_other1.512
r_angle_other_deg1.126
r_chiral_restr0.152
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_gen_planes_other0.007
r_bond_other_d0.002
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 Atoms1214
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing