X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A4G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M Bis-tris, 100 mM NaCl, 50 mM CaCl2, 22-24% PEG2000MME
Crystal Properties
Matthews coefficientSolvent content
2.1242.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.22α = 90
b = 107.65β = 90.19
c = 88.36γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.9800Photon FactoryBL-17A

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
12.75098.80.1428.43.141314
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)
12.72.85990.48233

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 REPLACEMENTTHROUGHOUT3A4G2.745.9739203209197.770.225630.222980.27494RANDOM28.475
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]
-1.887.431.470.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.841
r_dihedral_angle_3_deg17.795
r_dihedral_angle_4_deg15.897
r_dihedral_angle_1_deg5.769
r_long_range_B_refined1.472
r_angle_refined_deg1.327
r_mcangle_it0.201
r_mcbond_it0.108
r_chiral_restr0.081
r_scbond_it0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.841
r_dihedral_angle_3_deg17.795
r_dihedral_angle_4_deg15.897
r_dihedral_angle_1_deg5.769
r_long_range_B_refined1.472
r_angle_refined_deg1.327
r_mcangle_it0.201
r_mcbond_it0.108
r_chiral_restr0.081
r_scbond_it0.07
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12386
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms172

Software

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