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Crystal Structure of Cimex Nitrophorin Ferrous NO Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 PEG 4000, Li2SO4, ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.9 34.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49 α = 90 b = 41.56 β = 95.29 c = 65.37 γ = 90
Symmetry Space Group P 1 21 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 Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) 2004-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.9798 SSRL BL9-1
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 1.65 37.5 95.5 0.036 16.3 2.8 30416 30416 22.3
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) 1.65 1.71 83.5 0.186 4.2 2 2616
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 1NTF 1.65 30 28744 28744 1495 95.05 0.2054 0.2054 0.20314 0.209 0.24992 0.2615 RANDOM 23.84
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] 0.1 -1.85 0.12 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.141 r_dihedral_angle_3_deg 15.66 r_dihedral_angle_4_deg 13.648 r_dihedral_angle_1_deg 6.924 r_scangle_it 3.49 r_scbond_it 2.789 r_angle_refined_deg 1.918 r_mcangle_it 1.814 r_mcbond_it 1.539 r_angle_other_deg 1.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.141 r_dihedral_angle_3_deg 15.66 r_dihedral_angle_4_deg 13.648 r_dihedral_angle_1_deg 6.924 r_scangle_it 3.49 r_scbond_it 2.789 r_angle_refined_deg 1.918 r_mcangle_it 1.814 r_mcbond_it 1.539 r_angle_other_deg 1.297 r_mcbond_other 0.338 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.218 r_nbd_other 0.197 r_symmetry_vdw_other 0.197 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.114 r_symmetry_vdw_refined 0.099 r_nbtor_other 0.09 r_metal_ion_refined 0.07 r_xyhbond_nbd_other 0.049 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2242 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 45
Software Software Software Name Purpose Blu-Ice data collection d*TREK data reduction REFMAC refinement d*TREK data scaling