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1.00 A Crystal Structure Of L123V/L133V Mutant of Nitrophorin 4 From Rhodnius Prolixus Complexed With Imidazole at pH 5.6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X8O PDB entry 1X8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 300 ammonium phosphate, imidazole, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K
Crystal Properties Matthews coefficient Solvent content 1.53 19.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.221 α = 90 b = 42.743 β = 94.09 c = 52.886 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 IMAGE PLATE MAR scanner 345 mm plate Flat mirror (vertical focusing) 2002-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.751 SSRL BL9-1
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 19.81 97.4 0.04 0.04 20.8 3.23 81947 10
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 1.04 88 88.1 0.25 0.25 2.6 1.52 7330
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 1X8O 1 19.81 81937 81937 4145 97.39 0.145 0.145 0.144 0.1533 0.167 0.1705 RANDOM 8.376
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] 0.13 -0.16 0.13 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.95 r_dihedral_angle_3_deg 13.355 r_dihedral_angle_4_deg 7.792 r_dihedral_angle_1_deg 7.381 r_sphericity_free 7.035 r_sphericity_bonded 3.532 r_scangle_it 3.187 r_scbond_it 2.584 r_mcangle_it 1.896 r_angle_refined_deg 1.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.95 r_dihedral_angle_3_deg 13.355 r_dihedral_angle_4_deg 7.792 r_dihedral_angle_1_deg 7.381 r_sphericity_free 7.035 r_sphericity_bonded 3.532 r_scangle_it 3.187 r_scbond_it 2.584 r_mcangle_it 1.896 r_angle_refined_deg 1.658 r_rigid_bond_restr 1.596 r_mcbond_it 1.541 r_mcbond_other 1.031 r_angle_other_deg 0.889 r_nbd_refined 0.489 r_nbd_other 0.235 r_symmetry_vdw_other 0.211 r_nbtor_refined 0.186 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.148 r_chiral_restr 0.095 r_nbtor_other 0.088 r_metal_ion_refined 0.014 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1798 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 48
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection CrystalClear data scaling