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Crystal structure the Fab fragment of Efalizumab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B2W PDB ENTRY 1B2W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 15mM citric acid, 12% w/v PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.73 55.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.198 α = 90 b = 87.198 β = 90 c = 117.223 γ = 120
Symmetry Space Group P 31 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 IMAGE PLATE RIGAKU RAXIS IV++ Confocal 2007-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.8 20 98.1 0.083 0.083 6.3 7.2 48198 47282 1 1
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) 1.8 1.86 99.8 0.373 0.373 1.9 6.6 4699
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 ENTRY 1B2W 1.8 20 1 1 45884 44966 2347 98 0.1907 0.1907 0.18932 0.1978 0.21702 0.2079 RANDOM 21.482
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] -0.29 -0.15 -0.29 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.295 r_rigid_bond_restr 2.558 r_scangle_it 2.48 r_scbond_it 2.378 r_sphericity_free 2.141 r_angle_refined_deg 1.297 r_mcangle_it 1.151 r_sphericity_bonded 1.13 r_mcbond_it 0.664 r_nbd_refined 0.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.295 r_rigid_bond_restr 2.558 r_scangle_it 2.48 r_scbond_it 2.378 r_sphericity_free 2.141 r_angle_refined_deg 1.297 r_mcangle_it 1.151 r_sphericity_bonded 1.13 r_mcbond_it 0.664 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.156 r_symmetry_vdw_refined 0.149 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3274 Nucleic Acid Atoms Solvent Atoms 625 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection CNS refinement REFMAC refinement CrystalClear data reduction CrystalClear data scaling CNS phasing