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Crystal Structure of an Autonomous VH Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N8Z pdb entry 1N8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 1.1 M sodium malonate, 0.1 M Hepes, 0.5% Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.915 α = 109.97 b = 54.066 β = 95.64 c = 54.242 γ = 118.65
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1
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 1.8 50 96.2 0.039 43.2 4 40233
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 1.8 1.86 92.6 0.097 13.4 4 3886
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 MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1N8Z 1.8 20 38187 2023 95.98 0.157 0.155 0.1683 0.2 0.2109 RANDOM 19.485
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] 0.25 -0.1 0.38 -0.5 0.1 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.364 r_dihedral_angle_4_deg 18.4 r_dihedral_angle_3_deg 12.359 r_dihedral_angle_1_deg 6.143 r_scangle_it 5.093 r_mcangle_it 4.472 r_scbond_it 4.006 r_mcbond_it 3.75 r_angle_refined_deg 1.467 r_angle_other_deg 0.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.364 r_dihedral_angle_4_deg 18.4 r_dihedral_angle_3_deg 12.359 r_dihedral_angle_1_deg 6.143 r_scangle_it 5.093 r_mcangle_it 4.472 r_scbond_it 4.006 r_mcbond_it 3.75 r_angle_refined_deg 1.467 r_angle_other_deg 0.877 r_mcbond_other 0.721 r_symmetry_vdw_other 0.274 r_nbd_other 0.211 r_nbd_refined 0.199 r_nbtor_refined 0.189 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.104 r_symmetry_vdw_refined 0.092 r_nbtor_other 0.086 r_xyhbond_nbd_other 0.034 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3617 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection