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Minimal Recognition Complex between PrmA and Ribosomal Protein L11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NXC pdb entries 2NXC, 2NXN experimental model PDB 2NXN pdb entries 2NXC, 2NXN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 22% w/v PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.211 α = 90 b = 33.948 β = 131.76 c = 71.09 γ = 90
Symmetry Space Group C 1 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 ADSC QUANTUM 4 Variable vertical and fixed horizontal slits. KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit beam condition. Located ~18 m from source and ~6 m from sample position. Mirror system consisting of two vertically stacked, fused silica, spherical mirrors, to provide vertical focusing and harmonic rejection. One of the mirrors is rhodium coated and the other is uncoated. Located ~19.7 m from source. 2006-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.9797 NSLS X4A
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 1.37 30 95.1 0.053 22.5 3.2 37200 -3
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 1.37 1.42 84.7 0.386 2.6 2.8 3269
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 entries 2NXC, 2NXN 1.37 25.72 35338 1849 95.02 0.18166 0.18034 0.1799 0.20601 0.2054 RANDOM 19.711
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] 0.01 0.02 -0.03 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.258 r_dihedral_angle_4_deg 16.937 r_dihedral_angle_3_deg 11.368 r_dihedral_angle_1_deg 5.621 r_scangle_it 2.345 r_scbond_it 1.637 r_angle_refined_deg 1.28 r_mcangle_it 1.151 r_mcbond_it 0.708 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.258 r_dihedral_angle_4_deg 16.937 r_dihedral_angle_3_deg 11.368 r_dihedral_angle_1_deg 5.621 r_scangle_it 2.345 r_scbond_it 1.637 r_angle_refined_deg 1.28 r_mcangle_it 1.151 r_mcbond_it 0.708 r_nbtor_refined 0.311 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.184 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1485 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing