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Crystal structure of human RNase H2 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 0.1M MgCl2, 15% PEG 3350, 0.1M Bis-Tris (pH 5.5), and 2mM reduced glutathione, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.99 38.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.068 α = 105.9 b = 108.366 β = 103.71 c = 114.264 γ = 111.42
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 225 mm CCD 2009-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
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 3.1 50 97.1 0.107 2.8 63130 2 2 69.09
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 3.1 3.15 87.6 0.411 2.2 2.3
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 (Observed) 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 3KIO 3.1 44.1 62816 3206 0.2057 0.203 0.2164 0.2554 0.2728 RANDOM 64.38
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] 4.1188 -10.8887 8.0403 4.0317 -2.3204 -8.1505
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.23 t_omega_torsion 1.95 t_angle_deg 1.03 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.23 t_omega_torsion 1.95 t_angle_deg 1.03 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25729 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing BUSTER refinement HKL-2000 data reduction HKL-2000 data scaling