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Crystal structure of C. crescentus PNPase bound to RNase E recognition peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GME PDB ENTRY 3GME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 19% WT/V PEG 3350, 0.15 M DL-MALIC ACID
Crystal Properties Matthews coefficient Solvent content 3.01 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.439 α = 90 b = 157.439 β = 90 c = 302.379 γ = 120
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 CCD 2011-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.6 30 93.2 0.22 5.5 6.3 85896 2.4
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 2.6 2.74 94.8 0.58 2.4 6.2
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 3GME 2.6 30 75066 2322 89.96 0.21037 0.209 0.2087 0.25447 0.2534 RANDOM 59.002
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] 0.09 0.05 0.09 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.278 r_dihedral_angle_4_deg 22.289 r_dihedral_angle_3_deg 19.782 r_dihedral_angle_1_deg 7.934 r_angle_refined_deg 2.265 r_chiral_restr 0.144 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.278 r_dihedral_angle_4_deg 22.289 r_dihedral_angle_3_deg 19.782 r_dihedral_angle_1_deg 7.934 r_angle_refined_deg 2.265 r_chiral_restr 0.144 r_bond_refined_d 0.017 r_gen_planes_refined 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12436 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing