X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YS4PDB Entry: 1YS4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293100 mM MES pH 6.5 50 mM calcium acetate 20% PEG 3350 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2344.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.479α = 90
b = 78.686β = 90
c = 243.41γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
12.129.1294.60.08583.27777347773422
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)
12.12.1899.90.2543.93.58072

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry: 1YS42.129.117771977719394894.580.180.180.1780.221RANDOM12.421
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]
1.03-0.7-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.965
r_scangle_it1.825
r_angle_refined_deg1.104
r_scbond_it1.085
r_angle_other_deg0.76
r_mcangle_it0.578
r_mcbond_it0.302
r_nbd_other0.228
r_symmetry_vdw_other0.227
r_symmetry_hbond_refined0.189
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.965
r_scangle_it1.825
r_angle_refined_deg1.104
r_scbond_it1.085
r_angle_other_deg0.76
r_mcangle_it0.578
r_mcbond_it0.302
r_nbd_other0.228
r_symmetry_vdw_other0.227
r_symmetry_hbond_refined0.189
r_nbd_refined0.181
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.152
r_nbtor_other0.079
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10562
Nucleic Acid Atoms
Solvent Atoms1003
Heterogen Atoms

Software

Software
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction