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1.22 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) Deuteroporphyrin IX Complexed With Nitric Oxide at pH 5.6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X8O PDB entry 1X8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 300 ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K
Crystal Properties Matthews coefficient Solvent content 1.61 22.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.21 α = 90 b = 42.666 β = 94.27 c = 53.005 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 4 Bent conical Si-mirror (Rh coating) 2003-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.22 20.38 95.8 0.06 0.06 24.3 5.93 44702 11.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.22 1.26 95.8 96.1 0.18 0.18 10.6 5.74 4462
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 FREE R PDB entry 1X8O 1.22 20.38 44644 44644 2233 95.68 0.119 0.118 0.118 0.1196 0.148 0.1485 RANDOM 7.583
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] 0.15 0.06 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.03 r_dihedral_angle_3_deg 12.556 r_dihedral_angle_4_deg 9.032 r_sphericity_free 7.737 r_dihedral_angle_1_deg 7.387 r_scangle_it 3.809 r_scbond_it 3.13 r_sphericity_bonded 2.867 r_mcangle_it 2.095 r_mcbond_it 1.738
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.03 r_dihedral_angle_3_deg 12.556 r_dihedral_angle_4_deg 9.032 r_sphericity_free 7.737 r_dihedral_angle_1_deg 7.387 r_scangle_it 3.809 r_scbond_it 3.13 r_sphericity_bonded 2.867 r_mcangle_it 2.095 r_mcbond_it 1.738 r_angle_refined_deg 1.674 r_rigid_bond_restr 1.423 r_angle_other_deg 0.927 r_mcbond_other 0.608 r_nbd_refined 0.47 r_symmetry_vdw_other 0.252 r_nbd_other 0.23 r_metal_ion_refined 0.225 r_symmetry_vdw_refined 0.212 r_nbtor_refined 0.192 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.109 r_nbtor_other 0.089 r_xyhbond_nbd_other 0.016 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1714 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 85
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data scaling