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Crystal structure of HypB from Methanocaldococcus jannaschii in the triphosphate form, in complex with zinc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 175 mM maleic acid disodium salt, 52.5 mM HCl, 14% PEG3350, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 46.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.12 α = 90 b = 68.13 β = 90 c = 155.99 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2005-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9785 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 20 98.6 0.048 20.54 3.76 51141 51141 3 24.484
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.2 93.1 0.084 9.3 1.94 6342
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.1 19.92 27577 27577 1410 100 0.203 0.201 0.2028 0.242 0.2446 RANDOM 17.353
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] 0.33 0.02 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.66 r_dihedral_angle_4_deg 13.626 r_dihedral_angle_3_deg 13.26 r_dihedral_angle_1_deg 5.33 r_scangle_it 1.969 r_scbond_it 1.223 r_angle_refined_deg 1.09 r_mcangle_it 0.835 r_mcbond_it 0.528 r_nbtor_refined 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.66 r_dihedral_angle_4_deg 13.626 r_dihedral_angle_3_deg 13.26 r_dihedral_angle_1_deg 5.33 r_scangle_it 1.969 r_scbond_it 1.223 r_angle_refined_deg 1.09 r_mcangle_it 0.835 r_mcbond_it 0.528 r_nbtor_refined 0.29 r_symmetry_metal_ion_refined 0.232 r_symmetry_vdw_refined 0.187 r_nbd_refined 0.185 r_metal_ion_refined 0.12 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.072 r_symmetry_hbond_refined 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3246 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 70
Software Software Software Name Purpose XSCALE data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction