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Crystal Structure of PH0140 from Pyrococcus horikosii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CYY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.1 M HEPES (PH 7.5), 4.3 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.43 49.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.79 α = 90 b = 102.79 β = 90 c = 69.183 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2019-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 35 99.9 0.087 32.54 9.2 12806
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) 1 2 2.07 0.66
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2CYY 2.001 25.711 12806 646 99.86 0.175 0.1733 0.1831 0.2122 0.2145 30.418
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] -0.261 -0.261 0.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.452 r_dihedral_angle_4_deg 18.291 r_dihedral_angle_3_deg 15.144 r_dihedral_angle_1_deg 6.303 r_lrange_it 5.731 r_lrange_other 5.729 r_scangle_it 4.071 r_scangle_other 4.069 r_mcangle_it 2.879 r_mcangle_other 2.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.452 r_dihedral_angle_4_deg 18.291 r_dihedral_angle_3_deg 15.144 r_dihedral_angle_1_deg 6.303 r_lrange_it 5.731 r_lrange_other 5.729 r_scangle_it 4.071 r_scangle_other 4.069 r_mcangle_it 2.879 r_mcangle_other 2.877 r_scbond_it 2.736 r_scbond_other 2.734 r_mcbond_it 1.961 r_mcbond_other 1.959 r_angle_refined_deg 1.939 r_angle_other_deg 1.429 r_nbd_refined 0.281 r_symmetry_nbd_refined 0.269 r_nbd_other 0.214 r_symmetry_nbd_other 0.209 r_xyhbond_nbd_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.168 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1207 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing