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Structure of MAR1 Ribonuclease from Caenorhabditis elegans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X9G The starting model was created by the Swiss-Model Server based on PDB entry 1X9G using the C. elegans target sequence (F35G2.2)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 20% PEG3350, 0.2M sodium acetate, 0.1M Tris , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.2 44.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.545 α = 90 b = 113.973 β = 90 c = 151.322 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 103 IMAGE PLATE RIGAKU RAXIS IV Mirrors 2005-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.14 50 98.3 0.062 23.4 3.5 84631 84631 1 18.7
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) 2.14 2.22 94.7 0.168 3.3 8022
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT The starting model was created by the Swiss-Model Server based on PDB entry 1X9G using the C. elegans target sequence (F35G2.2) 2.141 41.67 78165 78165 4183 97.49 0.2217 0.2217 0.2195 0.2195 0.2627 RANDOM 25.126
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] -0.46 -0.89 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.471 r_dihedral_angle_4_deg 19.117 r_dihedral_angle_3_deg 13.68 r_dihedral_angle_1_deg 5.182 r_scangle_it 1.263 r_angle_refined_deg 1.058 r_scbond_it 0.795 r_mcangle_it 0.679 r_mcbond_it 0.399 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.471 r_dihedral_angle_4_deg 19.117 r_dihedral_angle_3_deg 13.68 r_dihedral_angle_1_deg 5.182 r_scangle_it 1.263 r_angle_refined_deg 1.058 r_scbond_it 0.795 r_mcangle_it 0.679 r_mcbond_it 0.399 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.102 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11856 Nucleic Acid Atoms Solvent Atoms 607 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling MOLREP phasing REFMAC refinement HKL-2000 data reduction