X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KCZPDB ENTRY 3KCZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.527725% PEG3350, 0.1M Tris
Crystal Properties
Matthews coefficientSolvent content
2.448.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.083α = 90
b = 134.123β = 117.96
c = 58.348γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.99190DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.13099.50.1090.10714.67.54585145851
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)
12.12.1598.40.6693.17.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3KCZ2.129.284355822931000.189840.187630.23103RANDOM27.879
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]
0.970.540.37-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.227
r_dihedral_angle_4_deg16.891
r_dihedral_angle_3_deg14.919
r_dihedral_angle_1_deg6.212
r_scangle_it3.724
r_scbond_it2.319
r_angle_refined_deg1.53
r_mcangle_it1.471
r_angle_other_deg1.027
r_mcbond_it0.805
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.227
r_dihedral_angle_4_deg16.891
r_dihedral_angle_3_deg14.919
r_dihedral_angle_1_deg6.212
r_scangle_it3.724
r_scbond_it2.319
r_angle_refined_deg1.53
r_mcangle_it1.471
r_angle_other_deg1.027
r_mcbond_it0.805
r_mcbond_other0.19
r_chiral_restr0.088
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.004
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_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 Atoms5609
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling