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CRYSTAL STRUCTURE OF THE HUMAN RNA guanylyltransferase and 5'- phosphatase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I9S PDB ENTRY 1I9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2 M POTASSIUM CITRATE
Crystal Properties Matthews coefficient Solvent content 2.2 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.4 α = 90 b = 161.6 β = 104.7 c = 60.7 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH MIRRORS 2005-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.6 47.9 90.4 0.08 10.29 3.79 133485 3
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 1.6 1.7 87.9 0.4 2.71 2.73
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1I9S 1.6 80.85 126725 6714 90.4 0.206 0.204 0.234 0.2416 RANDOM 28.35
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] 0.3 -0.12 0.82 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.784 r_dihedral_angle_3_deg 14.109 r_dihedral_angle_4_deg 10.792 r_dihedral_angle_1_deg 5.876 r_scangle_it 2.421 r_scbond_it 1.612 r_angle_refined_deg 1.342 r_mcangle_it 1.083 r_angle_other_deg 0.892 r_mcbond_it 0.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.784 r_dihedral_angle_3_deg 14.109 r_dihedral_angle_4_deg 10.792 r_dihedral_angle_1_deg 5.876 r_scangle_it 2.421 r_scbond_it 1.612 r_angle_refined_deg 1.342 r_mcangle_it 1.083 r_angle_other_deg 0.892 r_mcbond_it 0.702 r_symmetry_vdw_other 0.266 r_nbd_refined 0.204 r_nbd_other 0.179 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.177 r_symmetry_hbond_refined 0.134 r_symmetry_vdw_refined 0.107 r_chiral_restr 0.102 r_nbtor_other 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6215 Nucleic Acid Atoms Solvent Atoms 460 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing