X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PY3PDB entry 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
2.8656.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.521α = 90
b = 65.913β = 100.92
c = 56.966γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORMARRESEARCHmirrors2001-11-15MSINGLE 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
12.22088.40.038171.91667116671243.3
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)
12.22.25759.70.1624.11.7456

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 1py32.219.88166711580186988.310.22280.22280.220470.2646RANDOM31.703
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]
-1.46-0.543.82-2.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.583
r_dihedral_angle_4_deg21.128
r_dihedral_angle_3_deg19.548
r_dihedral_angle_1_deg6.926
r_scangle_it2.327
r_scbond_it1.538
r_angle_refined_deg1.52
r_mcangle_it1.041
r_mcbond_it0.618
r_symmetry_vdw_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.583
r_dihedral_angle_4_deg21.128
r_dihedral_angle_3_deg19.548
r_dihedral_angle_1_deg6.926
r_scangle_it2.327
r_scbond_it1.538
r_angle_refined_deg1.52
r_mcangle_it1.041
r_mcbond_it0.618
r_symmetry_vdw_refined0.304
r_nbtor_refined0.302
r_symmetry_hbond_refined0.28
r_nbd_refined0.208
r_xyhbond_nbd_refined0.186
r_chiral_restr0.108
r_bond_refined_d0.014
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2232
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing