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Structure of eukaryotic rnr large subunit R1 complexed with designed adp analog compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CVX PDB ENTRY 2CVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 100MM HEPES, PH7.5, 20-25% PEG 3350, 0.2M NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.02 39.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.528 α = 90 b = 116.915 β = 90 c = 64.065 γ = 90
Symmetry Space Group P 21 21 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 315 2006-12-12 M SINGLE WAVELENGTH 2 1 x-ray CCD MARMOSAIC 300 mm CCD 2007-03-10 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C 2 SYNCHROTRON APS BEAMLINE 23-ID-B APS 23-ID-B
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 2.1 50 99.3 0.164 8.47 6.9 47632
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 2.1 2.18 96.8 0.423 2.41 3.8
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 2CVX 2.1 38.84 45193 2409 99.3 0.254 0.252 0.254 0.29 0.2937 RANDOM 50.59
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] -2.17 -1.51 3.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.829 r_dihedral_angle_3_deg 18.786 r_dihedral_angle_4_deg 18.205 r_dihedral_angle_1_deg 7 r_scangle_it 2.799 r_scbond_it 2.034 r_angle_refined_deg 1.719 r_mcangle_it 1.288 r_mcbond_it 1.074 r_angle_other_deg 0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.829 r_dihedral_angle_3_deg 18.786 r_dihedral_angle_4_deg 18.205 r_dihedral_angle_1_deg 7 r_scangle_it 2.799 r_scbond_it 2.034 r_angle_refined_deg 1.719 r_mcangle_it 1.288 r_mcbond_it 1.074 r_angle_other_deg 0.939 r_xyhbond_nbd_other 0.272 r_symmetry_vdw_other 0.24 r_mcbond_other 0.217 r_nbd_refined 0.214 r_nbd_other 0.196 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.188 r_symmetry_vdw_refined 0.14 r_symmetry_hbond_refined 0.127 r_chiral_restr 0.113 r_nbtor_other 0.092 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5120 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 67
Software Software Software Name Purpose CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing