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Crystal structure of anti-basigin Fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MA3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1% n-Octyl-beta-D-glucoside, 0.1M sodium citrate tribasic dihydrate, 22% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.47 50.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.452 α = 90 b = 53.048 β = 105.047 c = 54.313 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 9M 2018-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.123 78.924 81.6 0.999 13.5 4.8 139276 13.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.123 1.194 0.575
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4ma3 1.123 36.4 1.37 139266 6810 81.6 0.1223 0.1209 0.1221 0.1503 0.1507 19.68
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.0871 f_angle_d 1.1777 f_chiral_restr 0.0904 f_bond_d 0.0099 f_plane_restr 0.0087
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3171 Nucleic Acid Atoms Solvent Atoms 698 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement autoPROC data processing STARANISO data processing MOLREP phasing Coot model building XDS data processing pointless data reduction Aimless data reduction