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Mutant Human Ribonuclease 1 (V52L, D53L, N56L, F59L)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RSA PDB ENTRY 7RSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 1.0M ammonium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.461 α = 90 b = 98.461 β = 90 c = 112.087 γ = 120
Symmetry Space Group P 61 2 2
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 4 2004-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 50 99.1 0.082 35.5 18.4 22154
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 2 2.07 91.9 0.496 1.9 6.3
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 7RSA 2 20 20937 1123 99.15 0.2091 0.20664 0.2036 0.25454 0.2524 RANDOM 50.662
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 -0.02 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.665 r_dihedral_angle_4_deg 23.493 r_dihedral_angle_3_deg 18.233 r_dihedral_angle_1_deg 7.822 r_scangle_it 4.625 r_scbond_it 3.211 r_angle_refined_deg 2.54 r_mcangle_it 1.814 r_mcbond_it 1.312 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.665 r_dihedral_angle_4_deg 23.493 r_dihedral_angle_3_deg 18.233 r_dihedral_angle_1_deg 7.822 r_scangle_it 4.625 r_scbond_it 3.211 r_angle_refined_deg 2.54 r_mcangle_it 1.814 r_mcbond_it 1.312 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.274 r_symmetry_hbond_refined 0.249 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.163 r_bond_refined_d 0.03 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1985 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing