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Structure of human signal regulatory protein (sirp) beta
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2UV3 PDB ENTRY 2UV3, CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 400 NL 25 MG/ML SIRP BETA PLUS 50 NL RESERVOIR (2.5 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS PROPANE PH 7.0) EQUILIBRATED AGAINST 95 UL OF RESERVOIR AT 20.5 C.
Crystal Properties Matthews coefficient Solvent content 2.2 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.166 α = 90 b = 65.172 β = 93.43 c = 58.113 γ = 90
Symmetry Space Group P 1 21 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 CCD MARRESEARCH MIRRORS 2007-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.19 50 100 0.06 36.3 8.7 76112 -3 10.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.21 99.7 0.57 3.3 6.6
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 2UV3, CHAIN A 1.19 32.11 72274 3809 99.9 0.14 0.139 0.1486 0.157 0.1669 RANDOM 11.37
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] -0.51 -0.18 0.01 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.001 r_dihedral_angle_4_deg 14.157 r_dihedral_angle_3_deg 11.581 r_dihedral_angle_1_deg 6.253 r_scangle_it 5.574 r_scbond_it 4.454 r_mcangle_it 3.456 r_mcbond_it 2.887 r_angle_refined_deg 1.263 r_angle_other_deg 0.748
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.001 r_dihedral_angle_4_deg 14.157 r_dihedral_angle_3_deg 11.581 r_dihedral_angle_1_deg 6.253 r_scangle_it 5.574 r_scbond_it 4.454 r_mcangle_it 3.456 r_mcbond_it 2.887 r_angle_refined_deg 1.263 r_angle_other_deg 0.748 r_symmetry_vdw_other 0.268 r_symmetry_vdw_refined 0.215 r_nbd_other 0.202 r_nbd_refined 0.175 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.126 r_symmetry_hbond_refined 0.123 r_nbtor_other 0.083 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1661 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing