X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PY5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293100 mM Imidazole 10% PEG 8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0840.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.771α = 90
b = 77.726β = 90
c = 90.07γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97949APS24-ID-C

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
11.73096.8319553195522
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7699.80.3835.45.63236

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1PY51.728.4523029630296161696.780.172140.172140.170330.20501RANDOM20.315
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]
-0.870.820.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.326
r_dihedral_angle_3_deg14.135
r_dihedral_angle_4_deg13.26
r_dihedral_angle_1_deg5.876
r_scangle_it4.143
r_scbond_it2.621
r_mcangle_it1.708
r_angle_refined_deg1.232
r_rigid_bond_restr1.224
r_mcbond_it0.955
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.326
r_dihedral_angle_3_deg14.135
r_dihedral_angle_4_deg13.26
r_dihedral_angle_1_deg5.876
r_scangle_it4.143
r_scbond_it2.621
r_mcangle_it1.708
r_angle_refined_deg1.232
r_rigid_bond_restr1.224
r_mcbond_it0.955
r_chiral_restr0.094
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2368
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms29

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling