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RNase crystals grown in loops/micromounts
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DH5 PDB entry: 3DH5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Crystals grown in loops 5.5 295 1.7M Ammonium sulfate, 2M NaCal, 0.1M Sodium acetate, pH 5.5, Crystals grown in loops, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.7 54.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.19 α = 90 b = 64.19 β = 90 c = 63.8 γ = 120
Symmetry Space Group P 32 2 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 MARMOSAIC 325 mm CCD 2009-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9795 SSRL BL11-1
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 1.5 29 99.9 0.081 16 6 24805 24805 -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 1.5 1.54 0.867 2.4 6 1820
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 PDB entry: 3DH5 1.5 30 23536 1269 99.96 0.17709 0.17628 0.1838 0.19256 0.2028 RANDOM 9.956
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] 0.09 0.05 0.09 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.554 r_dihedral_angle_4_deg 19.177 r_dihedral_angle_3_deg 11.386 r_dihedral_angle_1_deg 6.683 r_scangle_it 4.682 r_scbond_it 2.903 r_mcangle_it 2.051 r_angle_refined_deg 1.766 r_mcbond_it 1.156 r_angle_other_deg 0.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.554 r_dihedral_angle_4_deg 19.177 r_dihedral_angle_3_deg 11.386 r_dihedral_angle_1_deg 6.683 r_scangle_it 4.682 r_scbond_it 2.903 r_mcangle_it 2.051 r_angle_refined_deg 1.766 r_mcbond_it 1.156 r_angle_other_deg 0.927 r_mcbond_other 0.333 r_chiral_restr 0.102 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 951 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 9
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement XDS data reduction XDS data scaling