X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MQ4PDB entry 1MQ4 (residues 274-307 deleted).

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277Protein buffer: 50 mM HEPES, pH 7.5, 5 mM TCEP. Protein was incubated on ice with 5 mM ligand (1:20 dilution of 100 mM stock in H2O for AMPPNP or DMSO for PHA-680626) for 0.5-1 h, followed by a brief centrifugation step and drop setting at RT (0.5 microliter protein + 0.5 microliter reservoir solution consisting of 500 mM magnesium acetate, 10 % PEG 4000 and 0.3 mM zinc acetate for AMPPNP, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5752.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.958α = 90
b = 65.958β = 90
c = 154.045γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.445.90.06323.265.614898
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4971.60.3191.853.9817

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 1MQ4 (residues 274-307 deleted).2.445.91411675793.980.204630.203020.23534RANDOM22.44
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]
4.252.124.25-6.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.08
r_scangle_it1.823
r_angle_refined_deg1.246
r_scbond_it1.051
r_angle_other_deg0.887
r_mcangle_it0.796
r_mcbond_it0.421
r_symmetry_hbond_refined0.374
r_nbd_other0.217
r_symmetry_vdw_other0.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.08
r_scangle_it1.823
r_angle_refined_deg1.246
r_scbond_it1.051
r_angle_other_deg0.887
r_mcangle_it0.796
r_mcbond_it0.421
r_symmetry_hbond_refined0.374
r_nbd_other0.217
r_symmetry_vdw_other0.212
r_nbd_refined0.181
r_symmetry_vdw_refined0.171
r_xyhbond_nbd_refined0.164
r_chiral_restr0.149
r_nbtor_other0.082
r_metal_ion_refined0.042
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_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 Atoms2366
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing