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1.00 A Crystal Structure of D30N Mutant of Nitrophorin 4 from Rhodnius Prolixus Complexed with Nitric Oxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KOI PDB entry 1KOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 Ammonium Phosphate 3.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.96 37.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.431 α = 90 b = 42.729 β = 94.27 c = 53.124 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) 2002-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.900 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 10.6 95 0.073 0.073 17.2 5.12 85604 85604 3.398
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 1.02 99.1 0.124 0.124 3.5 3.06 8863
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 1KOI 1 9.68 85604 75616 4005 93.85 0.14281 0.14281 0.14193 0.1472 0.15924 0.1487 RANDOM 7.253
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] 0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.389 r_sphericity_free 3.724 r_scangle_it 3.019 r_sphericity_bonded 2.937 r_scbond_it 2.134 r_angle_other_deg 2.1 r_mcangle_it 2 r_angle_refined_deg 1.699 r_mcbond_it 1.327 r_rigid_bond_restr 1.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.389 r_sphericity_free 3.724 r_scangle_it 3.019 r_sphericity_bonded 2.937 r_scbond_it 2.134 r_angle_other_deg 2.1 r_mcangle_it 2 r_angle_refined_deg 1.699 r_mcbond_it 1.327 r_rigid_bond_restr 1.098 r_nbd_other 0.256 r_nbd_refined 0.226 r_symmetry_vdw_other 0.223 r_metal_ion_refined 0.216 r_symmetry_vdw_refined 0.167 r_symmetry_hbond_refined 0.13 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.103 r_nbtor_other 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1535 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data reduction d*TREK data scaling