X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.1341.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.15α = 92.45
b = 48.24β = 92.65
c = 87.79γ = 113.53
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.954495.80.04162.1550005

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 1PK61.9154755352841000.2190.2140.26RANDOM13.04
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]
-0.360.130.13-0.150.150.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.683
r_dihedral_angle_4_deg16.912
r_dihedral_angle_3_deg14.488
r_dihedral_angle_1_deg6.622
r_scangle_it2.483
r_scbond_it1.898
r_mcangle_it1.837
r_angle_refined_deg1.582
r_mcbond_it1.173
r_nbtor_refined0.328
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.683
r_dihedral_angle_4_deg16.912
r_dihedral_angle_3_deg14.488
r_dihedral_angle_1_deg6.622
r_scangle_it2.483
r_scbond_it1.898
r_mcangle_it1.837
r_angle_refined_deg1.582
r_mcbond_it1.173
r_nbtor_refined0.328
r_symmetry_vdw_refined0.301
r_symmetry_hbond_refined0.249
r_nbd_refined0.241
r_xyhbond_nbd_refined0.187
r_chiral_restr0.118
r_bond_refined_d0.015
r_gen_planes_refined0.007
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_refined
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6152
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling