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Crystal structure of human 4E10 Fab in complex with phosphatidylglycerol (06:0 PG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FX7 PDB ENTRY 2FX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 293 DROP CONTAINS 10 MG/ML 4E10 FAB, 10 MM PHOSPHATIDYLGLYCEROL (06:0 PG) MIXED 1:1 V/V WITH RESERVOIR SOLUTION OF 0.2 M SODIUM IODIDE, 20% PEG 3350, PH 6.0, VAPOR DIFFUSION, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.22 α = 90 b = 150.22 β = 90 c = 472.16 γ = 120
Symmetry Space Group P 61 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 110 PIXEL DECTRIS PILATUS 6M 2013-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.00000 SSRL BL12-2
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 3.96 48.907 95.5 0.303 5.2 4.43 27268 62.9
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 3.96 4.06 97.4 0.711 2.1 4.16
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB ENTRY 2FX7 3.96 48.907 1.34 27257 1362 95.6 0.246 0.244 0.2388 0.291 0.2831 Random selection 77.8
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] 2.4712 2.4712 -4.9423
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.705 f_angle_d 0.988 f_chiral_restr 0.049 f_plane_restr 0.006 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19205 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 148
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing