X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YC5PDB ENTRY 1YC5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.82932M NH4SO4, 2%PEG400, 0.1M Bis-Tris pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.2545.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.388α = 90
b = 136.266β = 119.87
c = 89.26γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2009-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1210097.10.0860.0869.53.712051412051430

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1YC5219.95211926911926912051000.20220.201560.26723RANDOM30.84
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]
0.01-0.01-0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.817
r_dihedral_angle_4_deg17.781
r_dihedral_angle_3_deg14.453
r_dihedral_angle_1_deg5.492
r_scangle_it3.478
r_scbond_it2.163
r_angle_refined_deg1.506
r_mcangle_it1.313
r_mcbond_it0.735
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.817
r_dihedral_angle_4_deg17.781
r_dihedral_angle_3_deg14.453
r_dihedral_angle_1_deg5.492
r_scangle_it3.478
r_scbond_it2.163
r_angle_refined_deg1.506
r_mcangle_it1.313
r_mcbond_it0.735
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12707
Nucleic Acid Atoms
Solvent Atoms961
Heterogen Atoms305

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling