☰ Navigation Tabs
Crystal structure of human germline antibody 5-51/O12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QOT PDB ENTRY 3QOT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 1.8 M ammonium sulfate, 0.1 M CHES, pH 9.5, 5% dioxane, cryoprotectant: 2.1 M ammonium sulfate, 0.1 M CHES, pH 9.5, 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.67 α = 90 b = 73.83 β = 90 c = 103.05 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 95 CCD RIGAKU SATURN 944 VARIMAX HF 2009-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.1 30 93.6 0.079 16.8 4.9 27026 27026 -3 26
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 2.1 2.16 89.8 0.278 5.7 3.5
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3QOT 2.1 15 25857 25857 1099 89.5 0.17316 0.17316 0.17116 0.1752 0.21989 0.2248 RANDOM 25.2
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] 0.01 -0.2 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.958 r_scbond_it 21.853 r_scangle_it 21.825 r_dihedral_angle_4_deg 12.478 r_dihedral_angle_3_deg 12.184 r_dihedral_angle_1_deg 5.886 r_mcangle_it 3.605 r_mcbond_it 2.008 r_angle_refined_deg 1.021 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.958 r_scbond_it 21.853 r_scangle_it 21.825 r_dihedral_angle_4_deg 12.478 r_dihedral_angle_3_deg 12.184 r_dihedral_angle_1_deg 5.886 r_mcangle_it 3.605 r_mcbond_it 2.008 r_angle_refined_deg 1.021 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3276 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 96
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling