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Crystal structure of murine B7-H3 extracellular domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BIS PDB ENTRY 3BIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 0.1 M HEPES, pH 7.5; 20% PEG-10000, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 5.7 78.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.92 α = 90 b = 100.92 β = 90 c = 188.18 γ = 120
Symmetry Space Group P 61 2 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 ADSC QUANTUM 315 2009-11-19 M SINGLE WAVELENGTH 2 1 x-ray M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9789 NSLS X29A 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.833 87.399 99.7 0.117 18.1 13.1 12250
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 2.97 3.13 100 0.8 0.8 1 13.7
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 PDB ENTRY 3BIS 2.97 30 11661 589 99.5 0.21712 0.21548 0.2175 0.24974 0.2513 RANDOM 72.265
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] -0.02 -0.02 -0.02 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.736 r_dihedral_angle_3_deg 21.034 r_dihedral_angle_4_deg 19.567 r_dihedral_angle_1_deg 8.35 r_angle_refined_deg 1.742 r_angle_other_deg 0.841 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.736 r_dihedral_angle_3_deg 21.034 r_dihedral_angle_4_deg 19.567 r_dihedral_angle_1_deg 8.35 r_angle_refined_deg 1.742 r_angle_other_deg 0.841 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1513 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 74
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection MOSFLM data reduction BALBES phasing