☰ Navigation Tabs
Crystal structure of nitrophorin 2 complex with pyrimidine
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 1.88 34.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.374 α = 90 b = 34.374 β = 90 c = 255.82 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 2005-11-11 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 23.4 91 0.08 32 5 29002 29002 16
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 73 0.68 2 4 4255
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 1.4 23.4 27530 27530 1472 90.98 0.1714 0.1714 0.16934 0.1776 0.21058 0.2208 RANDOM 14.402
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] -0.4 -0.4 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.126 r_dihedral_angle_3_deg 14.189 r_sphericity_free 10.185 r_dihedral_angle_1_deg 7.189 r_scangle_it 4.814 r_sphericity_bonded 4.285 r_scbond_it 3.797 r_mcangle_it 2.927 r_mcbond_it 2.342 r_rigid_bond_restr 2.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.126 r_dihedral_angle_3_deg 14.189 r_sphericity_free 10.185 r_dihedral_angle_1_deg 7.189 r_scangle_it 4.814 r_sphericity_bonded 4.285 r_scbond_it 3.797 r_mcangle_it 2.927 r_mcbond_it 2.342 r_rigid_bond_restr 2.002 r_angle_refined_deg 1.895 r_dihedral_angle_4_deg 1.608 r_angle_other_deg 1.527 r_mcbond_other 0.847 r_nbd_refined 0.208 r_symmetry_vdw_other 0.205 r_nbd_other 0.197 r_symmetry_hbond_refined 0.193 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_refined 0.166 r_chiral_restr 0.118 r_nbtor_other 0.093 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1442 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data reduction HKL-2000 data scaling