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Mcg immunoglobulin variable domain with methylene blue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UNU PDB ENTRY 4UNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.2 M NH4CL, 2.2 M (NH4)2SO4, 0.5 M METHYLENE BLUE, pH 8.5
Crystal Properties Matthews coefficient Solvent content 1.9 35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.22 α = 90 b = 31.08 β = 90.09 c = 73.63 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2014-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C APS 24-ID-C
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 1.05 40 89 0.07 10 3.5 73808 3
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 1.05 1.08 82 0.59 2.4 3.5
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 4UNU 1.05 39.22 78400 4102 98.81 0.11092 0.11033 0.12234 0.1341 RANDOM 16.864
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] -5.54 -1.58 5.44 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.715 r_dihedral_angle_4_deg 29.251 r_sphericity_free 26.787 r_dihedral_angle_3_deg 10.971 r_sphericity_bonded 8.157 r_rigid_bond_restr 7.427 r_dihedral_angle_1_deg 7.068 r_angle_refined_deg 3.272 r_scbond_it 2.642 r_angle_other_deg 2.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.715 r_dihedral_angle_4_deg 29.251 r_sphericity_free 26.787 r_dihedral_angle_3_deg 10.971 r_sphericity_bonded 8.157 r_rigid_bond_restr 7.427 r_dihedral_angle_1_deg 7.068 r_angle_refined_deg 3.272 r_scbond_it 2.642 r_angle_other_deg 2.182 r_mcangle_it 2.052 r_mcbond_other 2.03 r_mcbond_it 2.028 r_chiral_restr 0.244 r_bond_refined_d 0.046 r_gen_planes_refined 0.019 r_gen_planes_other 0.015 r_bond_other_d 0.007 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1596 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing