X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZYJPDB entry 1ZYJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.9293100 mM MES, 20-30% PEG4000, 50 mM n-BOG, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1442.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.785α = 90
b = 70.003β = 90
c = 74.513γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic2009-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54170

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
12.34099.70.0817.064.631631916273-324.163
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)
2.32.499.80.2566.34.651934

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 REPLACEMENTTHROUGHOUTPDB entry 1ZYJ2.333.88163191627181499.70.1990.1960.254RANDOM16.56
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]
-0.16-0.450.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.851
r_dihedral_angle_3_deg18.068
r_dihedral_angle_4_deg17.62
r_dihedral_angle_1_deg5.634
r_scangle_it2.743
r_scbond_it1.772
r_angle_refined_deg1.472
r_mcangle_it1.277
r_mcbond_it0.698
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.851
r_dihedral_angle_3_deg18.068
r_dihedral_angle_4_deg17.62
r_dihedral_angle_1_deg5.634
r_scangle_it2.743
r_scbond_it1.772
r_angle_refined_deg1.472
r_mcangle_it1.277
r_mcbond_it0.698
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2735
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms78

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling