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Crystal structure of JAML in complex with the stimulatory antibody HL4E10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 1.2-1.4 M NA-MALONATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.02 α = 90 b = 125.02 β = 90 c = 107.839 γ = 90
Symmetry Space Group P 43 21 2
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 MARMOSAIC 300 mm CCD SI(111) DOUBLE CRYSTAL MONOCHROMATOR. ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY 2006-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
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 2.95 30 97.7 0.122 0.122 6.8 3.1 18365
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) 2.95 3.06 99 0.617 0.617 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.95 30 17200 927 97.8 0.225 0.222 0.2232 0.287 0.2886 RANDOM 77.244
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] -1.23 -1.23 2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.308 r_dihedral_angle_4_deg 16.668 r_dihedral_angle_3_deg 15.482 r_dihedral_angle_1_deg 6.138 r_scangle_it 3.516 r_scbond_it 1.982 r_angle_other_deg 1.303 r_mcangle_it 1.217 r_angle_refined_deg 1.061 r_mcbond_it 0.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.308 r_dihedral_angle_4_deg 16.668 r_dihedral_angle_3_deg 15.482 r_dihedral_angle_1_deg 6.138 r_scangle_it 3.516 r_scbond_it 1.982 r_angle_other_deg 1.303 r_mcangle_it 1.217 r_angle_refined_deg 1.061 r_mcbond_it 0.606 r_symmetry_vdw_other 0.15 r_symmetry_vdw_refined 0.132 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.12 r_mcbond_other 0.071 r_chiral_restr 0.066 r_xyhbond_nbd_other 0.025 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4995 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 99
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling