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1.22 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) Deuteroporphyrin IX Complexed With Water at pH 5.6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X8Q PDB entry 1X8Q
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 1.56 20.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.288 α = 90 b = 42.699 β = 94.35 c = 52.979 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 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 21.35 95.7 0.07 0.07 15.3 6.19 44684 15.1
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 94 93.9 0.31 0.31 3.4 6.02 4353
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 1X8Q 1.22 20.38 44670 44670 2233 95.64 0.134 0.134 0.133 0.1355 0.167 0.168 RANDOM 10.368
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] 0.71 -0.27 0.06 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.331 r_dihedral_angle_3_deg 13.795 r_dihedral_angle_4_deg 9.112 r_sphericity_free 8.772 r_dihedral_angle_1_deg 7.355 r_scangle_it 4.282 r_sphericity_bonded 3.636 r_scbond_it 3.48 r_mcangle_it 2.328 r_mcbond_it 1.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.331 r_dihedral_angle_3_deg 13.795 r_dihedral_angle_4_deg 9.112 r_sphericity_free 8.772 r_dihedral_angle_1_deg 7.355 r_scangle_it 4.282 r_sphericity_bonded 3.636 r_scbond_it 3.48 r_mcangle_it 2.328 r_mcbond_it 1.908 r_angle_refined_deg 1.76 r_rigid_bond_restr 1.67 r_angle_other_deg 0.94 r_mcbond_other 0.705 r_nbd_refined 0.494 r_symmetry_vdw_refined 0.258 r_nbd_other 0.239 r_symmetry_vdw_other 0.193 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.151 r_chiral_restr 0.112 r_nbtor_other 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1769 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 78
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data scaling