X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PY4PDB ENTRY 2PY4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.52981.45 M Ammonium sulphate, 50 mM Tris, 12% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0539.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.228α = 90
b = 55.228β = 90
c = 83.65γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMIRRORS2008-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X12EMBL/DESY, HAMBURGX12

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
11.82099.90.06914.583.3913348-326.12
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)
11.81.8599.20.4712.412.54

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2PY41.819.161263868899.140.16020.157650.20733RANDOM16.224
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]
0.720.360.72-1.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.503
r_dihedral_angle_4_deg17.386
r_dihedral_angle_3_deg11.635
r_dihedral_angle_1_deg6.294
r_scangle_it4.979
r_scbond_it3.097
r_angle_other_deg2.592
r_mcangle_it1.866
r_angle_refined_deg1.741
r_mcbond_it1.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.503
r_dihedral_angle_4_deg17.386
r_dihedral_angle_3_deg11.635
r_dihedral_angle_1_deg6.294
r_scangle_it4.979
r_scbond_it3.097
r_angle_other_deg2.592
r_mcangle_it1.866
r_angle_refined_deg1.741
r_mcbond_it1.138
r_mcbond_other0.41
r_symmetry_vdw_other0.28
r_symmetry_hbond_refined0.197
r_xyhbond_nbd_refined0.16
r_symmetry_vdw_refined0.141
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_gen_planes_other0.001
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1046
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms45

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction