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Structure of the cytokine-like nuclear factor n-pac
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VPD PDB ENTRY 1VPD, 2I9P experimental model PDB 2I9P PDB ENTRY 1VPD, 2I9P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20% PEG3350 0.20 M KSCN
Crystal Properties Matthews coefficient Solvent content 3.2 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.18 α = 90 b = 134.18 β = 90 c = 261.463 γ = 120
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 MARRRESEARCH 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 2.5 47.7 99.8 0.15 8.93 5.61 60779
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 2.5 2.59 98.3 0.54 2.35 4.42
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1VPD, 2I9P 2.5 50 57621 3072 100 0.172 0.17 0.211 0.1977 RANDOM 29.62
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] 1.84 0.92 1.84 -2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.664 r_dihedral_angle_4_deg 16.436 r_dihedral_angle_3_deg 16.025 r_scangle_it 11.457 r_scbond_it 8.62 r_dihedral_angle_1_deg 5.181 r_mcangle_it 3.978 r_mcbond_it 2.051 r_angle_refined_deg 1.286 r_angle_other_deg 0.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.664 r_dihedral_angle_4_deg 16.436 r_dihedral_angle_3_deg 16.025 r_scangle_it 11.457 r_scbond_it 8.62 r_dihedral_angle_1_deg 5.181 r_mcangle_it 3.978 r_mcbond_it 2.051 r_angle_refined_deg 1.286 r_angle_other_deg 0.885 r_symmetry_vdw_other 0.362 r_nbd_refined 0.228 r_nbtor_refined 0.184 r_nbd_other 0.178 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.113 r_nbtor_other 0.089 r_chiral_restr 0.069 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8709 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing