X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293100 mM MES, 20-30% PEG4000, 50 mM n-BOG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3547.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.41α = 90
b = 74.66β = 90
c = 78.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateOsmic2008-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54170

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
11.954099.70.03330.394.662905428964-333.441
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)
1.952.0599.90.2177.74.573968

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 1ZYJ1.9540290542896386999.70.210.2090.254RANDOM29.886
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]
-0.01-0.580.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.973
r_dihedral_angle_4_deg20.886
r_dihedral_angle_3_deg16.359
r_dihedral_angle_1_deg5.718
r_scangle_it3.791
r_scbond_it2.487
r_mcangle_it1.736
r_angle_refined_deg1.503
r_mcbond_it1.11
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.973
r_dihedral_angle_4_deg20.886
r_dihedral_angle_3_deg16.359
r_dihedral_angle_1_deg5.718
r_scangle_it3.791
r_scbond_it2.487
r_mcangle_it1.736
r_angle_refined_deg1.503
r_mcbond_it1.11
r_nbtor_refined0.311
r_nbd_refined0.213
r_symmetry_vdw_refined0.21
r_symmetry_hbond_refined0.194
r_xyhbond_nbd_refined0.171
r_chiral_restr0.098
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2668
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms70

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling