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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 2 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.608 α = 90 b = 125.773 β = 90 c = 33.395 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 2004-04-08 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 1.4 26 92 0.09 20 5.5 31128 31128 20.9
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 93 0.25 1.5 3.8 3089
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 26 29280 1563 91.21 0.1794 0.1794 0.17755 0.187 0.21391 0.2198 RANDOM 21.996
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] -1.16 0.49 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.153 r_dihedral_angle_3_deg 16.229 r_sphericity_free 11.53 r_dihedral_angle_1_deg 7.288 r_dihedral_angle_4_deg 6.47 r_sphericity_bonded 5.723 r_scangle_it 5.624 r_scbond_it 4.34 r_mcangle_it 3.236 r_mcbond_it 2.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.153 r_dihedral_angle_3_deg 16.229 r_sphericity_free 11.53 r_dihedral_angle_1_deg 7.288 r_dihedral_angle_4_deg 6.47 r_sphericity_bonded 5.723 r_scangle_it 5.624 r_scbond_it 4.34 r_mcangle_it 3.236 r_mcbond_it 2.586 r_rigid_bond_restr 2.333 r_angle_refined_deg 1.988 r_angle_other_deg 1.585 r_mcbond_other 1.116 r_symmetry_vdw_other 0.222 r_symmetry_vdw_refined 0.212 r_xyhbond_nbd_refined 0.2 r_nbd_refined 0.198 r_nbd_other 0.19 r_nbtor_refined 0.183 r_chiral_restr 0.132 r_nbtor_other 0.096 r_symmetry_hbond_refined 0.087 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1422 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data reduction d*TREK data scaling