X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PY3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2298ammonium sulfate, phosphate buffer pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.9458.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.489α = 90
b = 67.313β = 100.63
c = 57.234γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORMARRESEARCHmirrors2003-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X311.1EMBL/DESY, HAMBURGX31

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
11.82098.90.05419.3351953476222
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)
11.81.8296.80.3172.71104

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 REPLACEMENTTHROUGHOUT1py31.8203476233012175098.780.217070.215480.24635RANDOM23.922
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]
-1.110.162.28-1.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.785
r_dihedral_angle_4_deg20.416
r_dihedral_angle_3_deg15.922
r_dihedral_angle_1_deg6.661
r_scangle_it2.389
r_scbond_it1.667
r_angle_refined_deg1.388
r_mcangle_it0.986
r_angle_other_deg0.931
r_mcbond_it0.809
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.785
r_dihedral_angle_4_deg20.416
r_dihedral_angle_3_deg15.922
r_dihedral_angle_1_deg6.661
r_scangle_it2.389
r_scbond_it1.667
r_angle_refined_deg1.388
r_mcangle_it0.986
r_angle_other_deg0.931
r_mcbond_it0.809
r_nbd_refined0.21
r_nbd_other0.21
r_symmetry_vdw_other0.204
r_xyhbond_nbd_refined0.181
r_nbtor_refined0.179
r_symmetry_hbond_refined0.178
r_mcbond_other0.176
r_symmetry_vdw_refined0.162
r_chiral_restr0.08
r_nbtor_other0.079
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2217
Nucleic Acid Atoms
Solvent Atoms277
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing