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Crystal structure the Fab fragment of matuzumab/EMD72000 (Fab72000)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L7I PDB id 1L7I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 1.8M ammonium sulfate, 0.1M MES, pH 6.5, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.79 31.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.821 α = 90 b = 61.377 β = 90 c = 102.675 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 210 2007-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.918 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.15 52.7 99.9 0.102 0.102 7.2 5.3 20191 20191
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 99.9 0.417 0.417 3.618 4.6 1971
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB id 1L7I 2.15 50 20127 20127 1029 99.2 0.226 0.226 0.224 0.2276 0.264 0.269 RANDOM 25.434
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] -1.2 1.35 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.502 r_dihedral_angle_4_deg 18.367 r_dihedral_angle_1_deg 18.277 r_dihedral_angle_3_deg 17.007 r_scangle_it 1.885 r_angle_refined_deg 1.329 r_mcangle_it 1.297 r_scbond_it 1.19 r_mcbond_it 0.832 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.502 r_dihedral_angle_4_deg 18.367 r_dihedral_angle_1_deg 18.277 r_dihedral_angle_3_deg 17.007 r_scangle_it 1.885 r_angle_refined_deg 1.329 r_mcangle_it 1.297 r_scbond_it 1.19 r_mcbond_it 0.832 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.275 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.218 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.107 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3097 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection