X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DKUPDB ENTRY 1DKU

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.652

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.055α = 90
b = 103.875β = 97.63
c = 127.161γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I711MAX III711

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
12.652099.70.237.43.667352
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)
12.652.7999.90.712.13.6

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 1DKU2.652063978337199.90.2710.2690.299RANDOM34.24
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]
-2.98-0.21-3.656.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.859
r_dihedral_angle_3_deg19.53
r_dihedral_angle_4_deg16.263
r_dihedral_angle_1_deg6.531
r_angle_other_deg3.703
r_scangle_it2.088
r_angle_refined_deg1.389
r_mcangle_it1.289
r_scbond_it1.286
r_mcbond_it0.714
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.859
r_dihedral_angle_3_deg19.53
r_dihedral_angle_4_deg16.263
r_dihedral_angle_1_deg6.531
r_angle_other_deg3.703
r_scangle_it2.088
r_angle_refined_deg1.389
r_mcangle_it1.289
r_scbond_it1.286
r_mcbond_it0.714
r_symmetry_vdw_other0.253
r_nbd_other0.239
r_nbd_refined0.218
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.161
r_symmetry_hbond_refined0.127
r_symmetry_vdw_refined0.123
r_nbtor_other0.118
r_chiral_restr0.073
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_gen_planes_other0.004
r_bond_other_d
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 Atoms14256
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing