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Crystal structure of DR2231, the MazG-like protein from Deinococcus radiodurans, Apo structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YEU PDB ENTRY 2YEU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.01M MAGNESIUM CHLORIDE,0.05M SODIUM CACODYLATE, PH 6.0, 1M LITHIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.85 56.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.778 α = 90 b = 110.828 β = 90 c = 166.11 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 CCD ADSC QUANTUM 315r TOROIDAL FOCUSING MIRROR 2009-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.7 20 99.8 0.08 16 5.7 137940 20.78
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 1.7 1.79 99.7 0.13 7.1 4.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2YEU 1.7 20 130621 6916 99.77 0.20993 0.20876 0.2319 0.2506 RANDOM 25.723
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] 0.85 0.93 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.036 r_dihedral_angle_4_deg 16.985 r_dihedral_angle_3_deg 13.501 r_dihedral_angle_1_deg 4.739 r_scangle_it 3.58 r_scbond_it 2.165 r_angle_refined_deg 1.389 r_mcangle_it 1.351 r_mcbond_it 0.764 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.036 r_dihedral_angle_4_deg 16.985 r_dihedral_angle_3_deg 13.501 r_dihedral_angle_1_deg 4.739 r_scangle_it 3.58 r_scbond_it 2.165 r_angle_refined_deg 1.389 r_mcangle_it 1.351 r_mcbond_it 0.764 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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_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 6804 Nucleic Acid Atoms Solvent Atoms 791 Heterogen Atoms 227
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement