☰ Navigation Tabs
Crystal structure of AT1412dm Fab fragment in complex with CD9 large extracellular loop
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293.15 PEG 1000, sodium chloride, sodium potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.58 52.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.776 α = 71.12 b = 89.858 β = 89.59 c = 91.533 γ = 85.96
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 EIGER X 4M 2017-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.2 84.8 92.6 0.199 0.231 0.117 0.984 5 3.9 104319
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 94.6 1.048 1.216 0.615 0.982 3.9
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 6RLM 2.2 84.8 98939 5338 92.6 0.2553 0.2537 0.2866 0.2681 RANDOM 29.944
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] -2.62 -0.09 0.84 2.94 -1.19 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.664 r_dihedral_angle_4_deg 22.121 r_dihedral_angle_3_deg 17.439 r_dihedral_angle_1_deg 7.87 r_angle_refined_deg 1.34 r_angle_other_deg 1.145 r_chiral_restr 0.05 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.664 r_dihedral_angle_4_deg 22.121 r_dihedral_angle_3_deg 17.439 r_dihedral_angle_1_deg 7.87 r_angle_refined_deg 1.34 r_angle_other_deg 1.145 r_chiral_restr 0.05 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15644 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 19
Software Software Software Name Purpose DIALS data reduction Aimless data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction