X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PKTPDB ENTRY 2PKT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% PEG3350 0.20 M KSCN
Crystal Properties
Matthews coefficientSolvent content
238

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.25α = 90
b = 36.474β = 99.15
c = 88.706γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2007-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.546.479.70.0417.22.6949917
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)
11.51.6370.381.980.83

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 2PKT1.55047380252779.80.1660.1630.215RANDOM16.84
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]
-0.97-0.560.720.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.926
r_dihedral_angle_4_deg21.015
r_dihedral_angle_3_deg12.659
r_scangle_it8.097
r_dihedral_angle_1_deg6.81
r_scbond_it6.178
r_mcangle_it4.2
r_mcbond_it3.169
r_angle_refined_deg1.48
r_angle_other_deg0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.926
r_dihedral_angle_4_deg21.015
r_dihedral_angle_3_deg12.659
r_scangle_it8.097
r_dihedral_angle_1_deg6.81
r_scbond_it6.178
r_mcangle_it4.2
r_mcbond_it3.169
r_angle_refined_deg1.48
r_angle_other_deg0.93
r_symmetry_vdw_other0.254
r_symmetry_hbond_refined0.206
r_nbd_refined0.204
r_nbd_other0.194
r_symmetry_vdw_refined0.186
r_xyhbond_nbd_refined0.171
r_nbtor_refined0.168
r_nbtor_other0.086
r_chiral_restr0.084
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3188
Nucleic Acid Atoms
Solvent Atoms460
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing