X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PK6PDB ENTRY 1PK6

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.1442.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.35α = 92.39
b = 48.33β = 92.6
c = 88.06γ = 113.57
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42008-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.2550830.0619.151.71673662
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)
11.251.472.10.295.41.05

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 1PK61.2519.7115897783681000.176290.174960.20176RANDOM13.543
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]
-0.44-0.170.21-0.620.150.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.566
r_dihedral_angle_3_deg11.193
r_dihedral_angle_4_deg10.278
r_dihedral_angle_1_deg6.339
r_sphericity_bonded2.314
r_sphericity_free1.958
r_scangle_it1.918
r_scbond_it1.433
r_angle_refined_deg1.095
r_mcangle_it1.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.566
r_dihedral_angle_3_deg11.193
r_dihedral_angle_4_deg10.278
r_dihedral_angle_1_deg6.339
r_sphericity_bonded2.314
r_sphericity_free1.958
r_scangle_it1.918
r_scbond_it1.433
r_angle_refined_deg1.095
r_mcangle_it1.068
r_rigid_bond_restr0.761
r_mcbond_it0.644
r_nbtor_refined0.307
r_symmetry_vdw_refined0.219
r_nbd_refined0.216
r_symmetry_hbond_refined0.181
r_xyhbond_nbd_refined0.164
r_metal_ion_refined0.095
r_chiral_restr0.07
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6120
Nucleic Acid Atoms
Solvent Atoms1054
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement