X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MZ7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52950.1 M lithium sulfate monohydrate, 0.1M sodium citrate tribasic dihydrate, and 20% w/v polyethylene glycol 1000 , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.652.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.686α = 90
b = 109.757β = 122.8
c = 92.951γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2013-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.10Photon FactoryBL-1A

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
12.2501000.06519.16.865099650991.51.540
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)
12.22.241000.6371.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4MZ72.250116173961677324799.90.195030.193620.222RANDOM50.537
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]
-2.64-0.132.370.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.355
r_dihedral_angle_4_deg17.481
r_dihedral_angle_3_deg14.925
r_long_range_B_refined6.831
r_long_range_B_other6.826
r_dihedral_angle_1_deg5.049
r_scangle_other4.888
r_mcangle_it3.751
r_mcangle_other3.751
r_scbond_other3.044
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.355
r_dihedral_angle_4_deg17.481
r_dihedral_angle_3_deg14.925
r_long_range_B_refined6.831
r_long_range_B_other6.826
r_dihedral_angle_1_deg5.049
r_scangle_other4.888
r_mcangle_it3.751
r_mcangle_other3.751
r_scbond_other3.044
r_scbond_it3.042
r_mcbond_it2.436
r_mcbond_other2.436
r_angle_refined_deg1.304
r_angle_other_deg0.937
r_chiral_restr0.072
r_bond_refined_d0.008
r_bond_other_d0.005
r_gen_planes_refined0.005
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 Atoms7968
Nucleic Acid Atoms
Solvent Atoms407
Heterogen Atoms182

Software

Software
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling