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Structure of Xac NPP for evaluation of refinement methodology
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GSN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1M Bis-Tris HCl, 19% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.97 37.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.049 α = 90 b = 78.62 β = 90 c = 129.953 γ = 90
Symmetry Space Group P 21 21 21
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 2005-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
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 1.4 50 87.2 0.136 110794 110794
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2GSN 1.45 39.9 93861 4886 82.24 0.18675 0.18547 0.1915 0.21063 0.2179 RANDOM 16.705
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] 0.06 -0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.207 r_dihedral_angle_3_deg 12.659 r_dihedral_angle_4_deg 11.314 r_dihedral_angle_1_deg 5.881 r_scangle_it 2.334 r_scbond_it 1.583 r_angle_refined_deg 1.294 r_mcangle_it 0.999 r_mcbond_it 0.87 r_angle_other_deg 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.207 r_dihedral_angle_3_deg 12.659 r_dihedral_angle_4_deg 11.314 r_dihedral_angle_1_deg 5.881 r_scangle_it 2.334 r_scbond_it 1.583 r_angle_refined_deg 1.294 r_mcangle_it 0.999 r_mcbond_it 0.87 r_angle_other_deg 0.82 r_symmetry_vdw_other 0.278 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.197 r_nbd_other 0.19 r_mcbond_other 0.184 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.116 r_nbtor_other 0.081 r_chiral_restr 0.079 r_metal_ion_refined 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5882 Nucleic Acid Atoms Solvent Atoms 669 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling