X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YY9PDB ENTRY 1YY9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298100 mM Na/K phosphate, pH 5.5, 40% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7955.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.426α = 90
b = 66.426β = 90
c = 203.868γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442008-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.27097.50.0620.572747726790-3
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)
12.22.2878.70.2194.53.3

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 1YY92.250.12746125334134597.150.18520.183130.22311RANDOM36.381
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]
0.430.220.43-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.701
r_dihedral_angle_4_deg22.116
r_dihedral_angle_3_deg15.06
r_dihedral_angle_1_deg7.06
r_scangle_it2.152
r_scbond_it1.561
r_angle_refined_deg1.372
r_mcangle_it0.92
r_angle_other_deg0.871
r_mcbond_it0.727
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.701
r_dihedral_angle_4_deg22.116
r_dihedral_angle_3_deg15.06
r_dihedral_angle_1_deg7.06
r_scangle_it2.152
r_scbond_it1.561
r_angle_refined_deg1.372
r_mcangle_it0.92
r_angle_other_deg0.871
r_mcbond_it0.727
r_symmetry_vdw_other0.214
r_symmetry_hbond_refined0.208
r_nbd_other0.199
r_nbd_refined0.189
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.172
r_symmetry_vdw_refined0.143
r_mcbond_other0.127
r_nbtor_other0.084
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3223
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms5

Software

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