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Crystal structure of a Fab fragment with its ligand peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GIR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M Imidazole-HCl pH 6.5, 2.1 M Ammonium Sulfate, 0.2 M Potassium/Sodium Tartrate
Crystal Properties Matthews coefficient Solvent content 2.16 43.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.05 α = 90 b = 65 β = 111.8 c = 67.13 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 CCD RAYONIX MX300HE 2014-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1.0 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.93 45 98.2 12.3 5.8 34050
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2.04
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 5GIR 1.93 44.99 32291 1700 98.71 0.18766 0.18614 0.1861 0.21604 0.2165 RANDOM 21.578
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] -0.23 0.27 -0.49 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.821 r_dihedral_angle_4_deg 16.37 r_dihedral_angle_3_deg 13.901 r_dihedral_angle_1_deg 6.412 r_long_range_B_refined 4.715 r_scbond_it 1.99 r_mcangle_it 1.875 r_angle_refined_deg 1.534 r_mcbond_it 1.158 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.821 r_dihedral_angle_4_deg 16.37 r_dihedral_angle_3_deg 13.901 r_dihedral_angle_1_deg 6.412 r_long_range_B_refined 4.715 r_scbond_it 1.99 r_mcangle_it 1.875 r_angle_refined_deg 1.534 r_mcbond_it 1.158 r_chiral_restr 0.101 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3305 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data processing XDS data scaling PHASER phasing