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
2.8957.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.221α = 90
b = 66.775β = 100.8
c = 57.07γ = 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
12.22090.20.055183.219754197542238.5
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)
12.22.25765.40.2124.72.9579

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 1py32.219.94197541689691393.240.21030.21030.207560.26237RANDOM19.761
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]
-1.07-0.042.56-1.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.865
r_dihedral_angle_4_deg25.711
r_dihedral_angle_3_deg16.304
r_dihedral_angle_1_deg6.623
r_scangle_it2.434
r_angle_other_deg1.707
r_scbond_it1.607
r_angle_refined_deg1.555
r_mcangle_it0.953
r_mcbond_it0.805
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.865
r_dihedral_angle_4_deg25.711
r_dihedral_angle_3_deg16.304
r_dihedral_angle_1_deg6.623
r_scangle_it2.434
r_angle_other_deg1.707
r_scbond_it1.607
r_angle_refined_deg1.555
r_mcangle_it0.953
r_mcbond_it0.805
r_symmetry_vdw_other0.239
r_nbd_other0.219
r_nbd_refined0.207
r_xyhbond_nbd_refined0.193
r_nbtor_refined0.181
r_symmetry_hbond_refined0.179
r_symmetry_vdw_refined0.15
r_chiral_restr0.144
r_mcbond_other0.13
r_nbtor_other0.088
r_bond_refined_d0.014
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 Atoms2233
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing