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1.07 A Crystal Structure of D30N 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 37.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.142 α = 90 b = 42.776 β = 94.05 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 cylindrical 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 0.900 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 19.83 97.6 0.056 0.056 24.2 5.37 67346 67346 5.48
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 96.8 0.201 0.201 9.1 5.22 6648
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 1.07 19.8 67346 63529 3386 96.92 0.15069 0.15069 0.14955 0.156 0.17199 0.158 RANDOM 8.156
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] -0.19 -0.03 0.1 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.896 r_sphericity_free 4.895 r_scangle_it 3.562 r_sphericity_bonded 3.381 r_scbond_it 2.501 r_mcangle_it 2.155 r_angle_other_deg 1.927 r_angle_refined_deg 1.759 r_mcbond_it 1.461 r_rigid_bond_restr 1.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.896 r_sphericity_free 4.895 r_scangle_it 3.562 r_sphericity_bonded 3.381 r_scbond_it 2.501 r_mcangle_it 2.155 r_angle_other_deg 1.927 r_angle_refined_deg 1.759 r_mcbond_it 1.461 r_rigid_bond_restr 1.343 r_symmetry_vdw_other 0.262 r_nbd_other 0.252 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.215 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.108 r_symmetry_hbond_refined 0.104 r_nbtor_other 0.088 r_metal_ion_refined 0.016 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1473 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data reduction d*TREK data scaling