2CMP

crystal structure of the DNA binding domain of G1P SMALL TERMINASE SUBUNIT from bacteriophage SF6


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293HANGING DROP WITH 1 UL OF 17MG/ML PROTEIN IN 50MM HEPES PH7.5 10MM NACL MIXED WITH 1 UL OF 2.4 M NA MALONATE PH 7.0 AND EQUILIBRATED AGAINST 1ML OF 2.4 M NA MALONATE PH 7.0 AT 20C
Crystal Properties
Matthews coefficientSolvent content
2.345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.286α = 90
b = 57.286β = 90
c = 57.286γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.5823.41000.0438.79.3878735.1
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)
11.581.6499.90.563.25.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.5840.52836340899.90.2270.2250.276RANDOM46.07
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.439
r_dihedral_angle_4_deg16.898
r_dihedral_angle_3_deg16.752
r_dihedral_angle_1_deg6.226
r_scangle_it5.781
r_scbond_it3.792
r_mcangle_it2.504
r_mcbond_it1.551
r_angle_refined_deg1.488
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.439
r_dihedral_angle_4_deg16.898
r_dihedral_angle_3_deg16.752
r_dihedral_angle_1_deg6.226
r_scangle_it5.781
r_scbond_it3.792
r_mcangle_it2.504
r_mcbond_it1.551
r_angle_refined_deg1.488
r_nbtor_refined0.31
r_nbd_refined0.283
r_symmetry_hbond_refined0.247
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.177
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.008
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_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 Atoms435
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing