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Crystal structure of the Ribonuclease H1 from Chlorobium tepidum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% PEG 4000, 0.1M sodium HEPES, 10% ispropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K 2 VAPOR DIFFUSION, HANGING DROP 5.4 298 26% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.457 α = 100.38 b = 33.388 β = 99.43 c = 66.072 γ = 90.82
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 325 mm CCD 2005-05-22 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r 2005-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 1.1158 SSRL BL11-1 2 SYNCHROTRON ALS BEAMLINE 8.3.1 0.9794 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.6 50 95.5 0.046 23.3 36214 36214
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.66 92.8 0.093 8.3
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 1.6 50 36214 33439 1758 95.52 0.16146 0.15969 0.2295 0.19362 0.2533 RANDOM 23.484
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 -1.07 -0.3 0.76 -0.57 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.664 r_dihedral_angle_4_deg 23.657 r_dihedral_angle_3_deg 13.941 r_sphericity_free 8.707 r_dihedral_angle_1_deg 6.65 r_scangle_it 4.461 r_scbond_it 3.259 r_sphericity_bonded 2.442 r_mcangle_it 2.001 r_mcbond_it 1.677
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.664 r_dihedral_angle_4_deg 23.657 r_dihedral_angle_3_deg 13.941 r_sphericity_free 8.707 r_dihedral_angle_1_deg 6.65 r_scangle_it 4.461 r_scbond_it 3.259 r_sphericity_bonded 2.442 r_mcangle_it 2.001 r_mcbond_it 1.677 r_rigid_bond_restr 1.55 r_angle_refined_deg 1.32 r_angle_other_deg 0.715 r_mcbond_other 0.519 r_symmetry_vdw_other 0.294 r_symmetry_hbond_refined 0.289 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.225 r_symmetry_vdw_refined 0.225 r_metal_ion_refined 0.211 r_nbd_other 0.194 r_xyhbond_nbd_other 0.187 r_nbtor_refined 0.183 r_chiral_restr 0.09 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2275 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement DENZO data reduction HKL-2000 data scaling