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RNase crystals grown by the hanging drop method
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DH5 Structure refinement using the data collected for the loop method (used PDB code: 3DH5 for MR for the loop method)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 1.7M Ammonium sulfate, 2M NaCal, 0.1M Sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.7 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.24 α = 90 b = 64.24 β = 90 c = 63.68 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 ADSC QUANTUM 315r 2009-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.9795 SSRL BL7-1
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 99.8 0.046 23.63 5.9 24750 24750 -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 0.446 3.9 5.8
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 Rigid body refinement THROUGHOUT Structure refinement using the data collected for the loop method (used PDB code: 3DH5 for MR for the loop method) 1.5 30 23475 1249 99.81 0.17665 0.17577 0.19335 0.1885 RANDOM 16.704
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] -0.04 -0.02 -0.04 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.285 r_dihedral_angle_4_deg 18.226 r_dihedral_angle_3_deg 12.337 r_dihedral_angle_1_deg 6.632 r_scangle_it 4.442 r_scbond_it 2.784 r_mcangle_it 2.046 r_angle_refined_deg 1.702 r_mcbond_it 1.151 r_angle_other_deg 0.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.285 r_dihedral_angle_4_deg 18.226 r_dihedral_angle_3_deg 12.337 r_dihedral_angle_1_deg 6.632 r_scangle_it 4.442 r_scbond_it 2.784 r_mcangle_it 2.046 r_angle_refined_deg 1.702 r_mcbond_it 1.151 r_angle_other_deg 0.932 r_mcbond_other 0.319 r_chiral_restr 0.105 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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 REFMAC refinement XDS data reduction XDS data scaling