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0.96 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) 2,4 Dimethyl 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 1.59 22.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.211 α = 90 b = 42.582 β = 94.61 c = 52.935 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 315 Bent conical Si-mirror (Rh coating) 2005-02-22 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 0.96 21.29 86.4 0.08 0.08 22.6 3.16 81981 11.5
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) 0.96 0.99 89 89 0.41 0.41 2.9 1.54 8392
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 21.29 72220 72220 3642 85.94 0.166 0.166 0.165 0.1664 0.195 0.1978 RANDOM 11.95
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] 0.27 0.03 0.03 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.275 r_dihedral_angle_3_deg 12.042 r_dihedral_angle_4_deg 8.299 r_dihedral_angle_1_deg 7.313 r_scangle_it 4.385 r_scbond_it 3.396 r_mcangle_it 2.397 r_angle_refined_deg 1.747 r_mcbond_it 1.739 r_nbd_refined 0.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.275 r_dihedral_angle_3_deg 12.042 r_dihedral_angle_4_deg 8.299 r_dihedral_angle_1_deg 7.313 r_scangle_it 4.385 r_scbond_it 3.396 r_mcangle_it 2.397 r_angle_refined_deg 1.747 r_mcbond_it 1.739 r_nbd_refined 0.418 r_nbtor_refined 0.31 r_metal_ion_refined 0.28 r_symmetry_vdw_refined 0.266 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.116 r_xyhbond_nbd_refined 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1722 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 48
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data scaling