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Crystal structure of a duf89 family protein (ph1575) from pyrococcus horikoshii at 2.04 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 4 277 10.0% MPD, 0.1M Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.73 54.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.859 α = 90 b = 88.859 β = 90 c = 81.499 γ = 120
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 QUANTUM 315 2005-12-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0000, 0.9796, 0.9797 ALS 8.2.2
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 2.04 40.76 99.7 0.067 12.28 3.78 45685 38.086
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 2.04 2.11 96.9 0.437 2.93 3.39
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.04 39.01 45659 2287 99.69 0.146 0.144 0.1542 0.182 0.1889 RANDOM 32.674
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] 1.38 0.69 1.38 -2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.59 r_dihedral_angle_4_deg 18.011 r_dihedral_angle_3_deg 13.124 r_scangle_it 8.029 r_dihedral_angle_1_deg 5.894 r_scbond_it 5.629 r_mcangle_it 3.045 r_mcbond_it 2.219 r_angle_refined_deg 1.345 r_angle_other_deg 0.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.59 r_dihedral_angle_4_deg 18.011 r_dihedral_angle_3_deg 13.124 r_scangle_it 8.029 r_dihedral_angle_1_deg 5.894 r_scbond_it 5.629 r_mcangle_it 3.045 r_mcbond_it 2.219 r_angle_refined_deg 1.345 r_angle_other_deg 0.767 r_mcbond_other 0.526 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.213 r_symmetry_vdw_other 0.201 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.168 r_nbd_other 0.167 r_nbtor_other 0.083 r_chiral_restr 0.08 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4442 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELX phasing autoSHARP phasing