☰ Navigation Tabs
Crystal Structure of Ribonucleotide Reductase apo-NrdF from Bacillus cereus (space group C2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DHZ PDB ENTRY 3DHZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.04 M H3PO4, 16% PEG 8000 AND 20% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.5 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.02 α = 90 b = 68.2 β = 106.01 c = 87.1 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 210 2010-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 34.2 99.4 0.1 11.1 3.3 34588 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 2.2 2.3 99.9 0.35 3.5 3.3
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 3DHZ 2.2 33.73 32842 1745 99.42 0.17906 0.17573 0.1763 0.24332 0.2426 RANDOM 25.624
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] -1.46 0.02 2.42 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.357 r_dihedral_angle_3_deg 19.228 r_dihedral_angle_4_deg 14.967 r_dihedral_angle_1_deg 5.968 r_scbond_it 3.321 r_mcangle_it 2.942 r_angle_refined_deg 2.006 r_mcbond_it 1.996 r_chiral_restr 0.159 r_bond_refined_d 0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.357 r_dihedral_angle_3_deg 19.228 r_dihedral_angle_4_deg 14.967 r_dihedral_angle_1_deg 5.968 r_scbond_it 3.321 r_mcangle_it 2.942 r_angle_refined_deg 2.006 r_mcbond_it 1.996 r_chiral_restr 0.159 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_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 4762 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing