X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AIK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1M Tris-HCl pH 8.5, 0.2M Ammonium phosphate monobasic, 50% MPD , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9257.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.213α = 90
b = 114.835β = 109.74
c = 102.219γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2010-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0SPring-8BL38B1

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
12.35098.90.1579.73.771172-3
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)
12.32.3898.30.3922.83.7

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 REPLACEMENTTHROUGHOUT3AIK2.332.4667472358896.660.211550.209630.24871RANDOM24.703
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]
0.981.68-0.931.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.182
r_dihedral_angle_4_deg19.167
r_dihedral_angle_3_deg19.024
r_dihedral_angle_1_deg8.37
r_scangle_it6.8
r_scbond_it4.682
r_mcangle_it2.771
r_mcbond_it1.701
r_angle_refined_deg0.897
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.182
r_dihedral_angle_4_deg19.167
r_dihedral_angle_3_deg19.024
r_dihedral_angle_1_deg8.37
r_scangle_it6.8
r_scbond_it4.682
r_mcangle_it2.771
r_mcbond_it1.701
r_angle_refined_deg0.897
r_chiral_restr0.079
r_gen_planes_refined0.017
r_bond_refined_d0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8940
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms105

Software

Software
Software NamePurpose
BL38B1data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling