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0.98 A crystal structure of nitrophorin 4 from Rhodnius prolixus containing FE(III) 2,4 dimethyl 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, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K
Crystal Properties Matthews coefficient Solvent content 1.57 20.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.873 α = 90 b = 42.49 β = 94.08 c = 52.633 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) 2005-02-23 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 0.98 20.28 85.5 0.08 0.08 30.3 4.52 75395 13.4
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) 0.98 1.02 72 0.4 0.4 4.3 2.04
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 0.98 20.3 75355 3769 85.5 0.167 0.165 0.1657 0.189 0.1883 RANDOM 13.95
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] 0.02 -0.26 -0.06 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.02 r_dihedral_angle_3_deg 12.115 r_dihedral_angle_1_deg 7.06 r_dihedral_angle_4_deg 6.927 r_sphericity_free 6.482 r_sphericity_bonded 3.857 r_scangle_it 3.637 r_scbond_it 2.931 r_angle_refined_deg 2.446 r_mcangle_it 2.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.02 r_dihedral_angle_3_deg 12.115 r_dihedral_angle_1_deg 7.06 r_dihedral_angle_4_deg 6.927 r_sphericity_free 6.482 r_sphericity_bonded 3.857 r_scangle_it 3.637 r_scbond_it 2.931 r_angle_refined_deg 2.446 r_mcangle_it 2.248 r_rigid_bond_restr 2.118 r_mcbond_it 1.573 r_nbd_refined 0.376 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.179 r_chiral_restr 0.171 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.145 r_metal_ion_refined 0.022 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1734 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement CrystalClear data scaling