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1.07 A crystal structure of L133V mutant of nitrophorin 4 from Rhodnius prolixus 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 1.62 23.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.32 α = 90 b = 42.847 β = 94.26 c = 52.871 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-FLAT SI-MIRROR (RH COATING) 2002-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D APS 14-BM-D
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 19.85 97.5 0.06 0.06 15.4 7.12 67479 10.9
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 98 0.3 0.3 4 6.79
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 1.07 19.8 67317 3416 97.3 0.141 0.139 0.1515 0.165 0.1724 RANDOM 8.69
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] 0.07 -0.02 -0.12 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.505 r_dihedral_angle_3_deg 12.807 r_dihedral_angle_4_deg 8.491 r_dihedral_angle_1_deg 7.791 r_sphericity_free 7.658 r_scangle_it 3.716 r_sphericity_bonded 3.229 r_scbond_it 3.073 r_mcangle_it 2.235 r_mcbond_it 1.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.505 r_dihedral_angle_3_deg 12.807 r_dihedral_angle_4_deg 8.491 r_dihedral_angle_1_deg 7.791 r_sphericity_free 7.658 r_scangle_it 3.716 r_sphericity_bonded 3.229 r_scbond_it 3.073 r_mcangle_it 2.235 r_mcbond_it 1.836 r_angle_refined_deg 1.743 r_rigid_bond_restr 1.467 r_angle_other_deg 0.889 r_mcbond_other 0.685 r_nbd_refined 0.417 r_nbd_other 0.22 r_symmetry_vdw_other 0.189 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.101 r_symmetry_hbond_refined 0.1 r_nbtor_other 0.091 r_symmetry_vdw_refined 0.085 r_xyhbond_nbd_other 0.049 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_metal_ion_refined 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 1712 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement CrystalClear data scaling d*TREK data scaling