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Crystal structure of the rNGFI-B ligand-binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PDU PDB ebtry 1PDU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 NaCl, BisTris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.86 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.422 α = 90 b = 90.422 β = 90 c = 140.637 γ = 90
Symmetry Space Group I 41 2 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 MARRESEARCH sagittal bender (mirror) 2003-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00003 SLS X06SA
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 2.4 40 98.3 0.058 20.8 8.5 11697 11676 1 1 66
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) 2.4 2.54 97.1 0.441 5.1 11676
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ebtry 1PDU 2.4 20 1 11676 11092 584 100 0.246 0.246 0.243 0.24 0.278 0.2718 RANDOM 67.445
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] 0.14 0.14 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.141 r_dihedral_angle_4_deg 25.118 r_dihedral_angle_3_deg 20.088 r_dihedral_angle_1_deg 6.542 r_scangle_it 3.323 r_scbond_it 2.148 r_mcangle_it 1.779 r_angle_refined_deg 1.521 r_mcbond_it 0.985 r_symmetry_hbond_refined 0.582
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.141 r_dihedral_angle_4_deg 25.118 r_dihedral_angle_3_deg 20.088 r_dihedral_angle_1_deg 6.542 r_scangle_it 3.323 r_scbond_it 2.148 r_mcangle_it 1.779 r_angle_refined_deg 1.521 r_mcbond_it 0.985 r_symmetry_hbond_refined 0.582 r_nbtor_refined 0.312 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1726 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling AMoRE phasing