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Crystal structure of human Cd11b I domain in C121 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 25% PEG Smear Medium
0.1M cacodylate pH 5.5
0.2M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.21 44.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.495 α = 90 b = 51.494 β = 132.961 c = 90.172 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS EIGER2 XE 16M 2022-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.11 65.99 92.5 0.981 7.5 6.4 23208
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.15 0.298
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.11 65.989 23208 1085 92.458 0.191 0.1883 0.2389 0.216 31.606
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] 1.069 1.006 -2.663 -0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.424 r_dihedral_angle_3_deg 14.443 r_dihedral_angle_4_deg 14.313 r_dihedral_angle_1_deg 7.295 r_lrange_it 6.101 r_lrange_other 6.097 r_scangle_it 4.557 r_scangle_other 4.556 r_mcangle_it 3.284 r_mcangle_other 3.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.424 r_dihedral_angle_3_deg 14.443 r_dihedral_angle_4_deg 14.313 r_dihedral_angle_1_deg 7.295 r_lrange_it 6.101 r_lrange_other 6.097 r_scangle_it 4.557 r_scangle_other 4.556 r_mcangle_it 3.284 r_mcangle_other 3.281 r_scbond_it 3.156 r_scbond_other 3.155 r_mcbond_it 2.324 r_mcbond_other 2.321 r_angle_refined_deg 1.609 r_angle_other_deg 1.283 r_nbd_other 0.211 r_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.187 r_xyhbond_nbd_refined 0.168 r_symmetry_nbd_refined 0.167 r_nbtor_refined 0.164 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2974 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing