X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JITPDB ENTRY 2JIT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1M HEPES 7.5, 0.3M NACL, 21% PEG6K, 5MM TCEP
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.405α = 90
b = 88.643β = 90
c = 164.867γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2007-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-CAPS24-ID-C

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
13.055099.80.117.55.814268-3
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)
13.053.2999.40.3944.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2JIT3.0524.121336671699.80.2140.2110.277RANDOM62.74
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]
0.09-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.566
r_dihedral_angle_3_deg19.449
r_dihedral_angle_4_deg16.542
r_dihedral_angle_1_deg5.391
r_scangle_it2.909
r_scbond_it1.654
r_mcangle_it1.484
r_angle_refined_deg1.367
r_mcbond_it0.785
r_nbtor_refined0.327
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.566
r_dihedral_angle_3_deg19.449
r_dihedral_angle_4_deg16.542
r_dihedral_angle_1_deg5.391
r_scangle_it2.909
r_scbond_it1.654
r_mcangle_it1.484
r_angle_refined_deg1.367
r_mcbond_it0.785
r_nbtor_refined0.327
r_nbd_refined0.258
r_symmetry_vdw_refined0.212
r_symmetry_hbond_refined0.205
r_xyhbond_nbd_refined0.171
r_chiral_restr0.083
r_bond_refined_d0.014
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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_other
r_long_range_B_refined
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 Atoms4787
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms33

Software

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