2WR8

Structure of Pyrococcus horikoshii SAM hydroxide adenosyltransferase in complex with SAH


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1719.83% PEG 6000, 0.26M KCL, 0.1M MOPS PH 7
Crystal Properties
Matthews coefficientSolvent content
141.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.561α = 90
b = 65.561β = 90
c = 142.685γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTORODIAL FOCUSING MIRROR2008-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.775099.70.0411.44.6223462
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)
11.771.831000.53.63.7

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 1WU81.7752.7821127113799.660.170390.167960.21739RANDOM33.439
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]
-1.57-0.78-1.572.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.946
r_dihedral_angle_4_deg17.436
r_dihedral_angle_3_deg13.528
r_dihedral_angle_1_deg6.654
r_scangle_it3.117
r_scbond_it2.331
r_angle_refined_deg1.623
r_mcangle_it1.301
r_mcbond_it1.146
r_angle_other_deg0.959
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.946
r_dihedral_angle_4_deg17.436
r_dihedral_angle_3_deg13.528
r_dihedral_angle_1_deg6.654
r_scangle_it3.117
r_scbond_it2.331
r_angle_refined_deg1.623
r_mcangle_it1.301
r_mcbond_it1.146
r_angle_other_deg0.959
r_symmetry_vdw_other0.266
r_mcbond_other0.261
r_symmetry_vdw_refined0.219
r_nbd_refined0.212
r_nbd_other0.211
r_nbtor_refined0.186
r_symmetry_hbond_refined0.163
r_xyhbond_nbd_refined0.15
r_nbtor_other0.109
r_chiral_restr0.098
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms2031
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing