X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.8293100 mM MES, 20-30% PEG4000, 50 mM n-BOG, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3848.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.71α = 90
b = 74.52β = 90
c = 78.91γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateOsmic2008-05-06MSINGLE 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
12.44099.90.06917.14.81594315927-339.99
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)
2.42.531000.3575.24.82264

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 1ZYJ2.434.87159431586995399.50.2080.2030.279RANDOM26.959
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]
-0.12-0.350.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.976
r_dihedral_angle_4_deg19.869
r_dihedral_angle_3_deg18.719
r_dihedral_angle_1_deg6.348
r_scangle_it3.294
r_scbond_it2.147
r_angle_refined_deg1.62
r_mcangle_it1.577
r_mcbond_it0.907
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.976
r_dihedral_angle_4_deg19.869
r_dihedral_angle_3_deg18.719
r_dihedral_angle_1_deg6.348
r_scangle_it3.294
r_scbond_it2.147
r_angle_refined_deg1.62
r_mcangle_it1.577
r_mcbond_it0.907
r_nbtor_refined0.313
r_nbd_refined0.221
r_symmetry_vdw_refined0.211
r_xyhbond_nbd_refined0.181
r_symmetry_hbond_refined0.171
r_chiral_restr0.1
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2660
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms50

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
MOSFLMdata reduction
SCALAdata scaling