X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NEKPDB ENTRY 1NEK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.50.1M TRIS PH8.5, 0.1M LI2SO4, 0.1M NACL, 0.009% DDM, 11% PEG4000
Crystal Properties
Matthews coefficientSolvent content
359

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.4α = 90
b = 178.46β = 90
c = 200.94γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.422.9699.70.110.23.61669376
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)
12.42.5399.90.52.63.5

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 1NEK2.4133.63158494838099.50.1720.1710.2RANDOM42.87
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]
-3.024.37-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.079
r_dihedral_angle_4_deg18.035
r_dihedral_angle_3_deg14.034
r_dihedral_angle_1_deg5.472
r_scangle_it3.628
r_scbond_it2.154
r_angle_refined_deg1.382
r_mcangle_it1.197
r_mcbond_it0.585
r_chiral_restr0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.079
r_dihedral_angle_4_deg18.035
r_dihedral_angle_3_deg14.034
r_dihedral_angle_1_deg5.472
r_scangle_it3.628
r_scbond_it2.154
r_angle_refined_deg1.382
r_mcangle_it1.197
r_mcbond_it0.585
r_chiral_restr0.15
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms24480
Nucleic Acid Atoms
Solvent Atoms1116
Heterogen Atoms438

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing