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Crystal structure of 5K RNase Sa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RGG PDB ENTRY 1RGG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 30% PEG4000, 200mM NaAcetate, 100mM Tris pH8.5, pH4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 40.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.339 α = 90 b = 46.241 β = 90 c = 36.744 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 100 IMAGE PLATE MAC Science DIP-3000 2003-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 50 98.7 0.084 8.4 11809
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 1RGG 1.6 29.88 11158 558 98 0.23129 0.2289 0.2258 0.28134 0.2792 RANDOM 22.147
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] -0.02 -0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.887 r_dihedral_angle_4_deg 23.707 r_dihedral_angle_3_deg 15.886 r_dihedral_angle_1_deg 7.243 r_scangle_it 5.355 r_scbond_it 4.041 r_mcangle_it 2.596 r_mcbond_it 1.829 r_angle_refined_deg 1.122 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.887 r_dihedral_angle_4_deg 23.707 r_dihedral_angle_3_deg 15.886 r_dihedral_angle_1_deg 7.243 r_scangle_it 5.355 r_scbond_it 4.041 r_mcangle_it 2.596 r_mcbond_it 1.829 r_angle_refined_deg 1.122 r_chiral_restr 0.095 r_gen_planes_refined 0.019 r_bond_refined_d 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 749 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling