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Crystal Structure of Ribonucleotide Reductase di-manganese(II) NrdF from Bacillus cereus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BMQ PDB ENTRY 4BMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2 M MG-FORMATE, 20% (W/V) PEG 3350, 0.1 M HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.1 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.88 α = 90 b = 49.21 β = 107.19 c = 98.52 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2010-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.9 47.06 90.4 0.11 11.3 2.1 40394 6
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 1.9 1.95 92.9 0.38 2.1 2.1
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 4BMQ 1.9 47.1 38342 2039 89.7 0.1865 0.184 0.1905 0.23313 0.2321 RANDOM 19.838
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] 0.24 -0.56 1.8 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.642 r_dihedral_angle_4_deg 21.186 r_dihedral_angle_3_deg 17.015 r_dihedral_angle_1_deg 5.37 r_scbond_it 2.828 r_mcangle_it 2.512 r_angle_refined_deg 1.895 r_mcbond_it 1.752 r_mcbond_other 1.745 r_angle_other_deg 1.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.642 r_dihedral_angle_4_deg 21.186 r_dihedral_angle_3_deg 17.015 r_dihedral_angle_1_deg 5.37 r_scbond_it 2.828 r_mcangle_it 2.512 r_angle_refined_deg 1.895 r_mcbond_it 1.752 r_mcbond_other 1.745 r_angle_other_deg 1.403 r_chiral_restr 0.158 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.006 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4650 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing