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1.08 A crystal structure of nitrophorin 4 from Rhodnius prolixus containing FE(III) deuteroporphyrin ix complexed with ammonia at ph 7.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X8P PDB ENTRY 1X8P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 300 AMMONIUM PHOSPHATE, pH 7.50, temperature 300.0K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 1.64 24.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.156 α = 90 b = 42.745 β = 94.03 c = 52.821 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) 2003-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 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 1.07 21.8 94.9 0.06 0.06 16.1 6.68 65307 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) 1.07 1.11 91 0.18 0.18 3.6 6.06
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1X8P 1.08 21.8 63622 3207 95.1 0.137 0.137 0.1498 0.162 0.1715 RANDOM 9.59
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] 0.24 -0.01 -0.45 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.451 r_dihedral_angle_3_deg 12.182 r_dihedral_angle_4_deg 8.623 r_sphericity_free 8.149 r_dihedral_angle_1_deg 7.343 r_scangle_it 3.809 r_sphericity_bonded 3.483 r_scbond_it 3.142 r_mcangle_it 2.355 r_mcbond_it 1.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.451 r_dihedral_angle_3_deg 12.182 r_dihedral_angle_4_deg 8.623 r_sphericity_free 8.149 r_dihedral_angle_1_deg 7.343 r_scangle_it 3.809 r_sphericity_bonded 3.483 r_scbond_it 3.142 r_mcangle_it 2.355 r_mcbond_it 1.915 r_angle_refined_deg 1.726 r_rigid_bond_restr 1.508 r_angle_other_deg 0.856 r_mcbond_other 0.715 r_nbd_refined 0.42 r_nbd_other 0.2 r_nbtor_refined 0.186 r_symmetry_vdw_other 0.172 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.13 r_chiral_restr 0.103 r_nbtor_other 0.087 r_symmetry_vdw_refined 0.064 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_metal_ion_refined 0.003 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1682 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement CrystalClear data scaling