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Crystal structure of D1A mutant of nitrophorin 2 complexed with ammonia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUO PDB ENTRY 1EUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 1mM protein, 3.2M ammonium phosphate, 100mM Tris HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.13 42.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.77 α = 90 b = 125.3 β = 90 c = 34.08 γ = 90
Symmetry Space Group P 21 21 2
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 Si-mirror 2004-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9000 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.2 6 88.5 0.14 9.2 8.6 47640 47640 14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.2 1.24 99.1 0.24 2.9 9.4 5261
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1EUO 1.2 6 45095 2426 88.32 0.17862 0.17862 0.17665 0.21512 0.2143 RANDOM 13.402
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 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.633 r_dihedral_angle_3_deg 13.448 r_sphericity_free 10.54 r_dihedral_angle_4_deg 7.734 r_dihedral_angle_1_deg 7.51 r_sphericity_bonded 5.084 r_scangle_it 4.71 r_scbond_it 3.97 r_mcangle_it 2.947 r_mcbond_it 2.635
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.633 r_dihedral_angle_3_deg 13.448 r_sphericity_free 10.54 r_dihedral_angle_4_deg 7.734 r_dihedral_angle_1_deg 7.51 r_sphericity_bonded 5.084 r_scangle_it 4.71 r_scbond_it 3.97 r_mcangle_it 2.947 r_mcbond_it 2.635 r_angle_refined_deg 2.083 r_rigid_bond_restr 2.003 r_mcbond_other 0.987 r_angle_other_deg 0.908 r_symmetry_vdw_other 0.27 r_nbd_refined 0.244 r_symmetry_vdw_refined 0.201 r_nbd_other 0.183 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.133 r_nbtor_other 0.095 r_bond_refined_d 0.021 r_gen_planes_refined 0.015 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1424 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data reduction d*TREK data scaling