X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6293100 mM MES, 20-30% PEG4000, 50 mM n-BOG, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2845.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.64α = 90
b = 74.06β = 93.9
c = 72γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMARRESEARCHDynamically bendable mirror2009-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.977032SLSX10SA

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
12.64099.50.11119.133.52299222870-336.301
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)
12.62.799.30.4995.43.492455

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 1ZYJ2.640229922286891599.50.1970.1940.271RANDOM17.587
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]
0.5-1.14-0.940.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.497
r_dihedral_angle_3_deg19.223
r_dihedral_angle_4_deg18.061
r_dihedral_angle_1_deg6.338
r_scangle_it2.641
r_scbond_it1.677
r_angle_refined_deg1.598
r_mcangle_it1.484
r_mcbond_it0.827
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.497
r_dihedral_angle_3_deg19.223
r_dihedral_angle_4_deg18.061
r_dihedral_angle_1_deg6.338
r_scangle_it2.641
r_scbond_it1.677
r_angle_refined_deg1.598
r_mcangle_it1.484
r_mcbond_it0.827
r_nbtor_refined0.317
r_nbd_refined0.233
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.182
r_symmetry_hbond_refined0.14
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5432
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms148

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling