2R25

Complex of YPD1 and SLN1-R1 with bound Mg2+ and BeF3-


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.62952.2 M ammonium sulfate, 50 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 5.60
Crystal Properties
Matthews coefficientSolvent content
2.8356.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.013α = 90
b = 75.544β = 90
c = 98.392γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42007-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12BNSLSX12B

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
11.65097.90.04828.86.151329
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)
1.61.7299.60.394.3

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1QSP1.717.754335342989216899.20.1990.1960.24RANDOM38.16
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.153
r_dihedral_angle_3_deg17.986
r_dihedral_angle_4_deg17.835
r_dihedral_angle_1_deg7.905
r_scangle_it6.306
r_scbond_it4.564
r_mcangle_it3.995
r_mcbond_it2.793
r_angle_refined_deg2.565
r_metal_ion_refined0.445
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.153
r_dihedral_angle_3_deg17.986
r_dihedral_angle_4_deg17.835
r_dihedral_angle_1_deg7.905
r_scangle_it6.306
r_scbond_it4.564
r_mcangle_it3.995
r_mcbond_it2.793
r_angle_refined_deg2.565
r_metal_ion_refined0.445
r_nbtor_refined0.311
r_nbd_refined0.26
r_symmetry_vdw_refined0.253
r_chiral_restr0.252
r_xyhbond_nbd_refined0.203
r_symmetry_hbond_refined0.142
r_bond_refined_d0.032
r_gen_planes_refined0.013
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_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 Atoms2479
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms6

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling