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Ribonucleotide Reductase R2_genomic protein from Aquifex aeolicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M citrate pH 4.0, 1.0 M lithium chloride, 20 % PEG6000
Crystal Properties Matthews coefficient Solvent content 2.53 51.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.246 α = 90 b = 69.246 β = 90 c = 177.57 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS EIGER2 X 16M 2021-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.1 47.247 100 1 22.9 25.7 26173
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 0.673
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7AIL 2.1 47.247 26093 1284 99.977 0.241 0.2378 0.2973 0.2518 62.164
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] 1.57 1.57 -3.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.143 r_dihedral_angle_4_deg 18.102 r_dihedral_angle_3_deg 17.707 r_lrange_it 9.598 r_lrange_other 9.553 r_mcangle_it 6.791 r_mcangle_other 6.789 r_scangle_it 6.778 r_scangle_other 6.777 r_dihedral_angle_1_deg 6.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.143 r_dihedral_angle_4_deg 18.102 r_dihedral_angle_3_deg 17.707 r_lrange_it 9.598 r_lrange_other 9.553 r_mcangle_it 6.791 r_mcangle_other 6.789 r_scangle_it 6.778 r_scangle_other 6.777 r_dihedral_angle_1_deg 6.495 r_mcbond_other 4.651 r_mcbond_it 4.65 r_scbond_it 4.444 r_scbond_other 4.442 r_angle_refined_deg 1.352 r_angle_other_deg 1.221 r_symmetry_xyhbond_nbd_refined 0.221 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.215 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.176 r_nbd_other 0.176 r_symmetry_nbd_refined 0.149 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.06 r_metal_ion_refined 0.054 r_symmetry_xyhbond_nbd_other 0.051 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2662 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing