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H71S mutant of the antibiotic resistance protein NimA from Deinococcus radiodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W3O PDB ENTRY 1W3O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 13MG/ML PROTEIN, 0.6M SODIUM ACETATE, 0.1M BUFFER PH 6 (CITRATE/MES).
Crystal Properties Matthews coefficient Solvent content 2.33 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.899 α = 90 b = 38.969 β = 113.89 c = 59.792 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 CCD MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.55 20 96.7 0.05 3.5 29814 16.6
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 1.55 1.63 79.8 0.54 2.8
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 1W3O 1.55 20 28320 1494 96.76 0.1839 0.18128 0.1874 0.23427 0.2358 RANDOM 12.861
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] 0.61 0.78 0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.699 r_dihedral_angle_4_deg 15.533 r_dihedral_angle_3_deg 14.316 r_dihedral_angle_1_deg 7.047 r_scangle_it 3.849 r_scbond_it 2.546 r_mcangle_it 1.816 r_angle_refined_deg 1.733 r_angle_other_deg 1.405 r_mcbond_it 1.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.699 r_dihedral_angle_4_deg 15.533 r_dihedral_angle_3_deg 14.316 r_dihedral_angle_1_deg 7.047 r_scangle_it 3.849 r_scbond_it 2.546 r_mcangle_it 1.816 r_angle_refined_deg 1.733 r_angle_other_deg 1.405 r_mcbond_it 1.062 r_mcbond_other 0.316 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 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_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 1651 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling