X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52778%-12% PEG 3000, 0.1 M acetate acid, pH 4.5, and 0.2 M zinc acetate
Crystal Properties
Matthews coefficientSolvent content
3.7266.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 222.468α = 90
b = 222.468β = 90
c = 209.46γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2013-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.979NSLSX4C

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
12.9940.7697.80.11825.47.3111753111753
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)
133.0598.60.4024.17.3

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 REPLACEMENTTHROUGHOUT4JNE2.9940.76111753590797.560.244890.242680.28701RANDOM76.682
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]
-1.28-1.28-1.284.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.004
r_dihedral_angle_3_deg16.276
r_dihedral_angle_4_deg14.456
r_long_range_B_refined11.602
r_long_range_B_other11.602
r_scangle_other8.052
r_mcangle_it7.926
r_mcangle_other7.926
r_dihedral_angle_1_deg6.728
r_scbond_it5.031
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.004
r_dihedral_angle_3_deg16.276
r_dihedral_angle_4_deg14.456
r_long_range_B_refined11.602
r_long_range_B_other11.602
r_scangle_other8.052
r_mcangle_it7.926
r_mcangle_other7.926
r_dihedral_angle_1_deg6.728
r_scbond_it5.031
r_scbond_other5.016
r_mcbond_it4.994
r_mcbond_other4.993
r_angle_refined_deg1.495
r_angle_other_deg0.805
r_chiral_restr0.098
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms28206
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms246

Software

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