3OQG

Restriction endonuclease HPY188I in complex with substrate DNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.22920.1 M MES/NaOH pH 6.2 and 30% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.4650.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.236α = 90
b = 65.236β = 90
c = 220.63γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHBENT MIRROR2010-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.05MPG/DESY, HAMBURGBW6

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
11.7520980.0610.06124.6515.55483304833023.2
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)
1.751.7797.10.440.443.2655.551895

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.7519.948287482872393980.166120.166120.164740.19218RESOLUTION SHELLS20.972
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]
0.70.7-1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.222
r_dihedral_angle_3_deg15.094
r_dihedral_angle_4_deg13.779
r_dihedral_angle_1_deg5.58
r_angle_other_deg3.961
r_scangle_it2.251
r_scbond_it1.492
r_angle_refined_deg1.224
r_mcangle_it1.107
r_mcbond_it0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.222
r_dihedral_angle_3_deg15.094
r_dihedral_angle_4_deg13.779
r_dihedral_angle_1_deg5.58
r_angle_other_deg3.961
r_scangle_it2.251
r_scbond_it1.492
r_angle_refined_deg1.224
r_mcangle_it1.107
r_mcbond_it0.6
r_nbd_other0.23
r_symmetry_vdw_other0.23
r_nbd_refined0.208
r_symmetry_vdw_refined0.208
r_nbtor_refined0.191
r_symmetry_hbond_refined0.182
r_xyhbond_nbd_other0.156
r_xyhbond_nbd_refined0.151
r_nbtor_other0.112
r_chiral_restr0.077
r_metal_ion_refined0.075
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.008
r_bond_other_d
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 Atoms2894
Nucleic Acid Atoms363
Solvent Atoms359
Heterogen Atoms3

Software

Software
Software NamePurpose
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing