2HF8

Crystal structure of HypB from Methanocaldococcus jannaschii in the triphosphate form, in complex with zinc


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION293175 mM maleic acid disodium salt, 52.5 mM HCl, 14% PEG3350, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2946.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.12α = 90
b = 68.13β = 90
c = 155.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9785ESRFID14-1

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
12.12098.60.04820.543.765114151141324.484
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)
2.12.293.10.0849.31.946342

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.119.92275772757714101000.2030.2010.242RANDOM17.353
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]
0.330.02-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.66
r_dihedral_angle_4_deg13.626
r_dihedral_angle_3_deg13.26
r_dihedral_angle_1_deg5.33
r_scangle_it1.969
r_scbond_it1.223
r_angle_refined_deg1.09
r_mcangle_it0.835
r_mcbond_it0.528
r_nbtor_refined0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.66
r_dihedral_angle_4_deg13.626
r_dihedral_angle_3_deg13.26
r_dihedral_angle_1_deg5.33
r_scangle_it1.969
r_scbond_it1.223
r_angle_refined_deg1.09
r_mcangle_it0.835
r_mcbond_it0.528
r_nbtor_refined0.29
r_symmetry_metal_ion_refined0.232
r_symmetry_vdw_refined0.187
r_nbd_refined0.185
r_metal_ion_refined0.12
r_xyhbond_nbd_refined0.115
r_chiral_restr0.072
r_symmetry_hbond_refined0.07
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3246
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms70

Software

Software
Software NamePurpose
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction