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E.coli RNase 1 in complex with d(CGCGATCGCG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PQX PDB ENTRY 2PQX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293 20% PEG8000, 0.1M Sodium acetate, 1mM MgCl2, 0.1M MES, pH6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.556 α = 90 b = 49.758 β = 90 c = 143.108 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 CCD MAR CCD 165 mm 2006-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8125 EMBL/DESY, HAMBURG X11
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 1.7 15 99.6 0.046 16.9 4.34 28734 28734
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 1.7 1.76 99.9 0.319 4.2 2813
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2PQX 1.7 15 28734 26505 2228 99.66 0.19363 0.19009 0.1883 0.2355 0.2334 RANDOM 21.326
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] -0.05 0.52 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.076 r_dihedral_angle_4_deg 18.579 r_dihedral_angle_3_deg 12.091 r_dihedral_angle_1_deg 6.019 r_scangle_it 3.313 r_scbond_it 2.207 r_mcangle_it 1.424 r_angle_refined_deg 1.357 r_mcbond_it 0.913 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.076 r_dihedral_angle_4_deg 18.579 r_dihedral_angle_3_deg 12.091 r_dihedral_angle_1_deg 6.019 r_scangle_it 3.313 r_scbond_it 2.207 r_mcangle_it 1.424 r_angle_refined_deg 1.357 r_mcbond_it 0.913 r_nbtor_refined 0.306 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.206 r_symmetry_hbond_refined 0.194 r_xyhbond_nbd_refined 0.176 r_metal_ion_refined 0.108 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1837 Nucleic Acid Atoms 68 Solvent Atoms 281 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing