2IKQ

Crystal structure of mouse Sts-1 PGM domain in complex with phosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION729314% PEG 8000, 0.1 M HEPES, 0.3 M Na Acetate, 0.2 M Na/K phosphate, pH 7.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3848.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.96α = 90
b = 74.671β = 100.79
c = 101.279γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26C1.0NSLSX26C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.609100980.630.63304.12566825668274.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.6092.6999.50.5560.5563.24.22582

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 SYNTHESISTHROUGHOUTPDB entry 1H0Q2.60999.52566424371129397.580.24910.247730.27515RANDOM68.359
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]
-4.21-1.428.82-5.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.681
r_dihedral_angle_4_deg20.943
r_dihedral_angle_3_deg19.431
r_dihedral_angle_1_deg6.359
r_scangle_it2.312
r_scbond_it1.494
r_angle_refined_deg1.42
r_mcangle_it1.294
r_mcbond_it0.707
r_symmetry_hbond_refined0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.681
r_dihedral_angle_4_deg20.943
r_dihedral_angle_3_deg19.431
r_dihedral_angle_1_deg6.359
r_scangle_it2.312
r_scbond_it1.494
r_angle_refined_deg1.42
r_mcangle_it1.294
r_mcbond_it0.707
r_symmetry_hbond_refined0.43
r_symmetry_vdw_refined0.367
r_nbtor_refined0.315
r_nbd_refined0.244
r_xyhbond_nbd_refined0.157
r_chiral_restr0.095
r_bond_refined_d0.011
r_gen_planes_refined0.004
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6103
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms15

Software

Software
Software NamePurpose
HKL-2000data collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing