X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZKJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.528920% PEG8000, 0.2M zinc acetate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2244.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.617α = 90
b = 59.378β = 102.19
c = 62.685γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702012-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.3861.27398.967316972411
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.381.39886.48

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1ZKJ1.5255708653733287499.160.164850.16360.18913RANDOM22.151
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]
0.161-1.260.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.974
r_dihedral_angle_4_deg13.357
r_sphericity_free12.74
r_dihedral_angle_3_deg10.508
r_rigid_bond_restr10.045
r_sphericity_bonded6.094
r_dihedral_angle_1_deg6.058
r_scbond_it1.7
r_mcangle_it1.607
r_angle_refined_deg1.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.974
r_dihedral_angle_4_deg13.357
r_sphericity_free12.74
r_dihedral_angle_3_deg10.508
r_rigid_bond_restr10.045
r_sphericity_bonded6.094
r_dihedral_angle_1_deg6.058
r_scbond_it1.7
r_mcangle_it1.607
r_angle_refined_deg1.321
r_mcbond_it1.053
r_mcbond_other1.036
r_angle_other_deg0.774
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.006
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_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2620
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms31

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection