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Crystal structure of nitrophorin 2 aqua complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.88 34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.754 α = 90 b = 125.642 β = 90 c = 33.468 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 2004-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 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 1.4 20 95.4 0.09 25 7.3 32453 32453 29.9
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) 1.4 1.45 98 0.47 2 6.4 3256
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1EUO 1.4 20 30813 1637 95.42 0.1872 0.1872 0.18479 0.1922 0.23279 0.2379 RANDOM 25.274
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] 1.06 -0.88 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.648 r_dihedral_angle_3_deg 16.006 r_sphericity_free 9.95 r_dihedral_angle_4_deg 8.535 r_dihedral_angle_1_deg 7.114 r_scangle_it 5.224 r_scbond_it 4.101 r_sphericity_bonded 4.084 r_rigid_bond_restr 3.717 r_mcangle_it 2.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.648 r_dihedral_angle_3_deg 16.006 r_sphericity_free 9.95 r_dihedral_angle_4_deg 8.535 r_dihedral_angle_1_deg 7.114 r_scangle_it 5.224 r_scbond_it 4.101 r_sphericity_bonded 4.084 r_rigid_bond_restr 3.717 r_mcangle_it 2.895 r_mcbond_it 2.313 r_angle_refined_deg 2.028 r_angle_other_deg 1.451 r_mcbond_other 0.84 r_symmetry_vdw_refined 0.368 r_symmetry_vdw_other 0.311 r_symmetry_hbond_refined 0.238 r_nbd_refined 0.204 r_nbd_other 0.186 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.131 r_nbtor_other 0.092 r_bond_refined_d 0.022 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1442 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data reduction d*TREK data scaling