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Crystal structure of nitrophorin 2 complex with NO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUO PDB ENTRY 1EUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 39.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.295 α = 90 b = 125.444 β = 90 c = 33.196 γ = 90
Symmetry Space Group P 21 21 2
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 4 bent Si-mirror 2003-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9000 APS 14-BM-C
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 1.45 22.8 89.3 0.093 13.2 4.4 26809 26809 17.1
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) 1.45 1.5 98.1 0.246 2.3 4.5 2879
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1EUO 1.45 22.8 25400 25400 1291 88.91 0.19488 0.19488 0.19291 0.1996 0.23462 0.1938 RANDOM 20.273
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] -0.22 -0.28 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.605 r_sphericity_free 6.293 r_scangle_it 5.003 r_sphericity_bonded 3.848 r_scbond_it 3.538 r_mcangle_it 2.896 r_angle_refined_deg 1.989 r_rigid_bond_restr 1.967 r_mcbond_it 1.926 r_angle_other_deg 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.605 r_sphericity_free 6.293 r_scangle_it 5.003 r_sphericity_bonded 3.848 r_scbond_it 3.538 r_mcangle_it 2.896 r_angle_refined_deg 1.989 r_rigid_bond_restr 1.967 r_mcbond_it 1.926 r_angle_other_deg 0.89 r_symmetry_vdw_refined 0.348 r_nbd_other 0.266 r_symmetry_vdw_other 0.246 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.142 r_chiral_restr 0.121 r_nbtor_other 0.091 r_metal_ion_refined 0.062 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1416 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction CCP4 data scaling