X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OOY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52936-10% PEG 3350, 0.1M Sodium Citrate, pH 5.5, 5mM ADP, 5mM AMP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.293α = 90
b = 78.087β = 124.13
c = 108.553γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97926APS24-ID-C

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
12.75096.80.1077.43.4319343091811
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)
12.72.881.60.4721.52.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2ooy2.748.283091829358155896.310.21060.206410.28945RANDOM52.865
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]
-1.7-1.58-0.570.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.552
r_dihedral_angle_3_deg20.538
r_dihedral_angle_4_deg18.171
r_dihedral_angle_1_deg7.039
r_scangle_it2.139
r_angle_refined_deg1.609
r_scbond_it1.322
r_mcangle_it0.928
r_mcbond_it0.526
r_nbtor_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.552
r_dihedral_angle_3_deg20.538
r_dihedral_angle_4_deg18.171
r_dihedral_angle_1_deg7.039
r_scangle_it2.139
r_angle_refined_deg1.609
r_scbond_it1.322
r_mcangle_it0.928
r_mcbond_it0.526
r_nbtor_refined0.321
r_nbd_refined0.239
r_symmetry_vdw_refined0.203
r_xyhbond_nbd_refined0.184
r_symmetry_hbond_refined0.115
r_chiral_restr0.112
r_bond_refined_d0.015
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8349
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing