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Ribonucleotide Reductase R2m protein from Aquifex aeolicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CI4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M citrate pH 4.0, 1.0 M lithium chloride, 20 % PEG6000
Crystal Properties Matthews coefficient Solvent content 2.55 51.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.409 α = 90 b = 69.409 β = 90 c = 178.292 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 PILATUS 6M 2015-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9762 Diamond I04
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 1.73 69.4 100 0.99 17.4 10.3 46576
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 1.73 1.77 0.81
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ci4 1.73 54.83 43386 2297 98.28 0.22507 0.22277 0.26739 0.2482 RANDOM 39.824
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] 1.17 1.17 -2.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.38 r_dihedral_angle_4_deg 17.491 r_dihedral_angle_3_deg 16.822 r_long_range_B_refined 7.572 r_long_range_B_other 7.544 r_dihedral_angle_1_deg 6.18 r_scangle_other 6.051 r_mcangle_it 4.603 r_mcangle_other 4.602 r_scbond_it 4.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.38 r_dihedral_angle_4_deg 17.491 r_dihedral_angle_3_deg 16.822 r_long_range_B_refined 7.572 r_long_range_B_other 7.544 r_dihedral_angle_1_deg 6.18 r_scangle_other 6.051 r_mcangle_it 4.603 r_mcangle_other 4.602 r_scbond_it 4.018 r_scbond_other 4.017 r_mcbond_it 3.405 r_mcbond_other 3.394 r_angle_refined_deg 1.535 r_angle_other_deg 1.337 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2723 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing