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Crystal structure of HypB from Methanocaldococcus jannaschii in the triphosphate form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HF8 PDB entry: 2Hf8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 150 mM maleic acid
disodium salt, 42.5 mM HCl, 20% PEG3350, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.463 α = 90 b = 68.107 β = 90 c = 155.84 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 ADSC 2005-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9758 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 6.5 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 6.4 6342
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry: 2Hf8 1.9 19.96 37222 37222 3723 100 0.22 0.217 0.2164 0.241 0.2416 RANDOM 16.316
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] 0.8 -0.28 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.368 r_dihedral_angle_4_deg 17.76 r_dihedral_angle_3_deg 13.069 r_dihedral_angle_1_deg 5.269 r_scangle_it 1.732 r_angle_refined_deg 1.104 r_scbond_it 1.032 r_mcangle_it 0.733 r_mcbond_it 0.439 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.368 r_dihedral_angle_4_deg 17.76 r_dihedral_angle_3_deg 13.069 r_dihedral_angle_1_deg 5.269 r_scangle_it 1.732 r_angle_refined_deg 1.104 r_scbond_it 1.032 r_mcangle_it 0.733 r_mcbond_it 0.439 r_nbtor_refined 0.293 r_nbd_refined 0.185 r_symmetry_metal_ion_refined 0.162 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.123 r_metal_ion_refined 0.119 r_symmetry_hbond_refined 0.082 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3246 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 68
Software Software Software Name Purpose XSCALE data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction