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1.15 A Crystal Structure of T121V Mutant of Nitrophorin 4 from Rhodnius Prolixus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D2U PDB entry 1D2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 Ammonium Phosphate 3.2 M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.95 37.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.3 α = 90 b = 42.763 β = 93.66 c = 52.89 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) 2002-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.900 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 1.15 21.37 97.1 0.05 0.05 20.8 3.19 54132 54132 5.78
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) 1.15 1.19 98.6 0.134 0.134 6 2.51 5460
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 THROUGHOUT PDB entry 1D2U 1.15 21.37 54132 50570 2727 95.62 0.1428 0.1428 0.14128 0.1466 0.17179 0.1504 RANDOM 8.884
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 -0.12 -0.22 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.836 r_sphericity_free 5.273 r_scangle_it 3.648 r_sphericity_bonded 3.241 r_scbond_it 2.612 r_mcangle_it 2.347 r_angle_other_deg 1.868 r_angle_refined_deg 1.829 r_mcbond_it 1.531 r_rigid_bond_restr 1.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.836 r_sphericity_free 5.273 r_scangle_it 3.648 r_sphericity_bonded 3.241 r_scbond_it 2.612 r_mcangle_it 2.347 r_angle_other_deg 1.868 r_angle_refined_deg 1.829 r_mcbond_it 1.531 r_rigid_bond_restr 1.473 r_nbd_refined 0.346 r_nbd_other 0.253 r_symmetry_vdw_other 0.242 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.116 r_symmetry_hbond_refined 0.089 r_nbtor_other 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1475 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data reduction d*TREK data scaling