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Crystal Structure of PH1978 from Pyrococcus horikoshii OT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 295 PEG 4000, CHES, pH 8.5, microbatch, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.6 28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.196 α = 90 b = 55.317 β = 90 c = 77.481 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 IMAGE PLATE RIGAKU RAXIS V RH coated bent-cylindrical mirror 2004-02-28 M SINGLE WAVELENGTH 2 1 x-ray IMAGE PLATE RIGAKU RAXIS V 2004-05-29 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1 2 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0, 0.97946, 0.97914 SPring-8 BL26B1
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 1.85 40 98.8 0.065 11.6 4.7 18717 18477 20.03
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 1.85 1.92 99.8 0.277
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 MAD THROUGHOUT 1.85 27.66 18717 18477 993 98.75 0.219 0.219 0.2271 0.259 0.2436 RANDOM 19.351
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] -1.09 1.66 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.899 r_scangle_it 3.019 r_scbond_it 1.656 r_angle_other_deg 1.068 r_mcangle_it 1.011 r_angle_refined_deg 0.96 r_mcbond_it 0.514 r_symmetry_vdw_other 0.299 r_nbd_other 0.219 r_nbd_refined 0.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.899 r_scangle_it 3.019 r_scbond_it 1.656 r_angle_other_deg 1.068 r_mcangle_it 1.011 r_angle_refined_deg 0.96 r_mcbond_it 0.514 r_symmetry_vdw_other 0.299 r_nbd_other 0.219 r_nbd_refined 0.187 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.125 r_symmetry_vdw_refined 0.114 r_nbtor_other 0.081 r_chiral_restr 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1874 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing