1GPP

Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.830 % PEG4000, 0.1 M SODIUM CITRATE PH 5.6, 0.2 M NH4-ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.856α = 90
b = 47.595β = 121.41
c = 60.297γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2001-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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
11.352094.10.02934.52.551602
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)
11.351.3764.10.1642.51.5

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 1VDE1.352047840374494.30.1530.150.189RANDOM19.93
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]
-1.97-0.611.92-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.1
r_scangle_it5.758
r_dihedral_angle_1_deg5.345
r_scbond_it3.838
r_mcangle_it2.979
r_mcbond_it2.004
r_angle_refined_deg1.834
r_angle_other_deg0.952
r_symmetry_hbond_refined0.44
r_nbd_refined0.262
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.1
r_scangle_it5.758
r_dihedral_angle_1_deg5.345
r_scbond_it3.838
r_mcangle_it2.979
r_mcbond_it2.004
r_angle_refined_deg1.834
r_angle_other_deg0.952
r_symmetry_hbond_refined0.44
r_nbd_refined0.262
r_symmetry_vdw_refined0.245
r_xyhbond_nbd_refined0.241
r_nbd_other0.2
r_symmetry_vdw_other0.192
r_chiral_restr0.159
r_xyhbond_nbd_other0.089
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1726
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing