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Crystal structure of ferrous cimex nitrophorin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NTF PDB ENTRY 1NTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 23% PEG 4000, 100 mM Tris HCl, 200 mM lithium sulfate, 15% ethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.107 α = 90 b = 41.491 β = 95.4 c = 65.38 γ = 90
Symmetry Space Group P 1 21 1
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-mirrors 2005-02-22 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 Merge 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 1.3 28.4 99.3 0.067 17.6 7.8 64243 64243 23.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.3 1.35 99.8 0.33 2.4 5.2 6369
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 1NTF 1.3 28.35 60962 60962 3250 99.26 0.17753 0.17753 0.17583 0.1776 0.20844 0.2086 RANDOM 20.918
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] 0.07 -0.97 0.37 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.46 r_dihedral_angle_4_deg 15.609 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_1_deg 6.747 r_scangle_it 5.31 r_scbond_it 4.194 r_mcangle_it 2.913 r_mcbond_it 2.397 r_angle_refined_deg 1.754 r_mcbond_other 1.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.46 r_dihedral_angle_4_deg 15.609 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_1_deg 6.747 r_scangle_it 5.31 r_scbond_it 4.194 r_mcangle_it 2.913 r_mcbond_it 2.397 r_angle_refined_deg 1.754 r_mcbond_other 1.675 r_angle_other_deg 0.905 r_symmetry_vdw_other 0.25 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.208 r_nbd_other 0.197 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.119 r_symmetry_hbond_refined 0.097 r_nbtor_other 0.088 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2251 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement ADSC data collection CrystalClear data reduction CrystalClear data scaling