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Crystal structure analysis of the dimeric form of the SRCR domain of mouse MARCO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OY3 PDB ENTRY 2OY3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 7% PEG 4000, 0.1M Bis-Tris, 0.1M Lithium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.99 38.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.087 α = 116.3 b = 36.553 β = 90.35 c = 44.605 γ = 96.41
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 MAR CCD 130 mm 2003-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.09700 MAX II I711
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 1.77 14.912 95.4 0.037 0.037 13.8 3.5 17081 16364 0.013
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 1.77 1.86 89.4 0.074 0.074 9.1 3.4 2282
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2OY3 1.77 14.912 17081 16364 1644 95.81 0.154 0.15 0.1491 0.191 0.1905 RANDOM 11.59
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] -0.01 -0.18 -0.04 0.08 -0.06 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.828 r_dihedral_angle_4_deg 14.79 r_dihedral_angle_3_deg 10.453 r_dihedral_angle_1_deg 6.313 r_scangle_it 3.098 r_scbond_it 2.137 r_angle_refined_deg 1.248 r_mcangle_it 1.203 r_mcbond_it 0.761 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.828 r_dihedral_angle_4_deg 14.79 r_dihedral_angle_3_deg 10.453 r_dihedral_angle_1_deg 6.313 r_scangle_it 3.098 r_scbond_it 2.137 r_angle_refined_deg 1.248 r_mcangle_it 1.203 r_mcbond_it 0.761 r_nbtor_refined 0.296 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1584 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 15
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling