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X-ray Structure of synthetic [D83A]RNase A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IZP PDB entry 1IZP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.89 0.1 M Bis-Tris, 1.0 M ammonium sulfate, 1.5 M NaCl, pH 5.89,
Drop 1:1 well:protein solution in H2O, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.71 54.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.59 α = 90 b = 63.59 β = 90 c = 63.365 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 300 mm CCD ADJUSTABLE FOCUSING MIRRORS 2006-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.05 20 59512
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 1IZP 1.1 20 56514 2998 98.45 0.17773 0.17693 0.172 0.19319 0.1898 RANDOM 14.452
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] 0.21 0.11 0.21 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.234 r_dihedral_angle_4_deg 20.319 r_dihedral_angle_3_deg 12.098 r_dihedral_angle_1_deg 6.375 r_sphericity_bonded 5.058 r_scangle_it 3.101 r_scbond_it 2.377 r_mcangle_it 2.146 r_angle_refined_deg 1.625 r_mcbond_it 1.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.234 r_dihedral_angle_4_deg 20.319 r_dihedral_angle_3_deg 12.098 r_dihedral_angle_1_deg 6.375 r_sphericity_bonded 5.058 r_scangle_it 3.101 r_scbond_it 2.377 r_mcangle_it 2.146 r_angle_refined_deg 1.625 r_mcbond_it 1.458 r_rigid_bond_restr 1.422 r_nbtor_refined 0.308 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 974 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement