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Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PFR pdb entry 1PFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 PEG 4000, 0.1M MES, 0.4M NACL, 1mM EMTS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.08 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.04 α = 90 b = 84.74 β = 90 c = 115.03 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 1997-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A 0.873 ESRF BM1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 19.6 99.1 0.084 10.8 3.3 57178 17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 98.4 0.233 6.8
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 1PFR 1.9 19.46 54865 2312 99.18 0.17449 0.17314 0.1814 0.20601 0.2134 RANDOM 16.662
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] -0.82 0.31 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.339 r_dihedral_angle_4_deg 15.278 r_dihedral_angle_3_deg 14.547 r_dihedral_angle_1_deg 5.143 r_scangle_it 2.823 r_scbond_it 1.99 r_angle_refined_deg 1.353 r_mcangle_it 1.153 r_mcbond_it 0.997 r_angle_other_deg 0.897
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.339 r_dihedral_angle_4_deg 15.278 r_dihedral_angle_3_deg 14.547 r_dihedral_angle_1_deg 5.143 r_scangle_it 2.823 r_scbond_it 1.99 r_angle_refined_deg 1.353 r_mcangle_it 1.153 r_mcbond_it 0.997 r_angle_other_deg 0.897 r_metal_ion_refined 0.257 r_nbd_refined 0.227 r_symmetry_vdw_other 0.22 r_xyhbond_nbd_refined 0.18 r_nbd_other 0.178 r_mcbond_other 0.175 r_symmetry_hbond_refined 0.165 r_symmetry_vdw_refined 0.126 r_nbtor_other 0.086 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5578 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling XFIT data reduction