X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22932.2 M ammonium sulfate, phosphate buffer pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0640.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.192α = 90
b = 62.648β = 129.18
c = 68.299γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORMARRESEARCHmirrors2001-11-16MSINGLE 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
12.252096.90.1111.43.5168701634722
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)
12.252.28750.3252.22.4491

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 REPLACEMENTTHROUGHOUT1py32.2520155261552682196.40.201670.198550.25921RANDOM9.666
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]
1.941.45-0.05-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.94
r_dihedral_angle_4_deg21.946
r_dihedral_angle_3_deg19.149
r_dihedral_angle_1_deg7.496
r_scangle_it2.164
r_angle_refined_deg1.604
r_scbond_it1.349
r_mcangle_it0.952
r_mcbond_it0.575
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.94
r_dihedral_angle_4_deg21.946
r_dihedral_angle_3_deg19.149
r_dihedral_angle_1_deg7.496
r_scangle_it2.164
r_angle_refined_deg1.604
r_scbond_it1.349
r_mcangle_it0.952
r_mcbond_it0.575
r_nbtor_refined0.305
r_symmetry_vdw_refined0.287
r_nbd_refined0.223
r_xyhbond_nbd_refined0.192
r_symmetry_hbond_refined0.141
r_chiral_restr0.106
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3030
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms137

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing