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Crystal Structure of C139A nostoc H-NOX domain with imidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 1.9M sodium malonate, pH 7.0,
Crystal Properties Matthews coefficient Solvent content 3.7 66.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.051 α = 90 b = 123.051 β = 90 c = 123.051 γ = 90
Symmetry Space Group P 21 3
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 MARMOSAIC 325 mm CCD Mirrors 2012-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97945 SSRL BL9-2
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 2.5 43.51 99.45 0.049 24.2 6.2 20550 59.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 100 2.3 6.3
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 4IAM 2.5 43.51 20550 1109 99.45 0.13282 0.13056 0.1348 0.17353 0.1735 RANDOM 59.313
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] -17.46 8.93 -22.17 -19 -18.58 36.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.8 r_dihedral_angle_4_deg 18.839 r_dihedral_angle_3_deg 18.602 r_long_range_B_refined 10.029 r_long_range_B_other 10.028 r_scangle_other 7.422 r_mcangle_other 6.763 r_mcangle_it 6.756 r_dihedral_angle_1_deg 6.143 r_scbond_it 5.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.8 r_dihedral_angle_4_deg 18.839 r_dihedral_angle_3_deg 18.602 r_long_range_B_refined 10.029 r_long_range_B_other 10.028 r_scangle_other 7.422 r_mcangle_other 6.763 r_mcangle_it 6.756 r_dihedral_angle_1_deg 6.143 r_scbond_it 5.33 r_scbond_other 5.33 r_mcbond_it 4.68 r_mcbond_other 4.615 r_angle_refined_deg 1.718 r_angle_other_deg 0.897 r_chiral_restr 0.135 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2864 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing