☰ Navigation Tabs
Crystal structure of nitrophorin 2 aqua complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PEE PDB ENTRY 1PEE
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 1.68 26.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.526 α = 90 b = 34.526 β = 90 c = 255.76 γ = 90
Symmetry Space Group P 41 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 2004-08-05 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 1.7 18.52 99.1 0.07 20 4.9 18316 18316 34.7
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) 1.7 1.76 99.2 0.38 2 3.8 1792
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 1PEE 1.7 18.52 17246 17246 917 99.15 0.1833 0.1833 0.18113 0.1903 0.22551 0.2347 RANDOM 23.485
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 -0.19 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.888 r_dihedral_angle_3_deg 13.981 r_dihedral_angle_4_deg 9.184 r_dihedral_angle_1_deg 6.991 r_scangle_it 3.779 r_sphericity_bonded 3.259 r_scbond_it 2.833 r_mcangle_it 1.915 r_angle_refined_deg 1.911 r_mcbond_it 1.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.888 r_dihedral_angle_3_deg 13.981 r_dihedral_angle_4_deg 9.184 r_dihedral_angle_1_deg 6.991 r_scangle_it 3.779 r_sphericity_bonded 3.259 r_scbond_it 2.833 r_mcangle_it 1.915 r_angle_refined_deg 1.911 r_mcbond_it 1.644 r_angle_other_deg 1.428 r_mcbond_other 0.35 r_symmetry_vdw_other 0.237 r_nbd_refined 0.184 r_nbd_other 0.18 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.158 r_symmetry_vdw_refined 0.14 r_chiral_restr 0.121 r_nbtor_other 0.088 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1432 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data reduction d*TREK data scaling