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Crystal structure analysis of the monomeric SRCR domain of mouse MARCO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BY2 PDB ENTRY 1BY2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 12% PEG 8000, 0.1M Bis-Tris, 0.2M Ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.69 27.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.345 α = 90 b = 28.06 β = 99.19 c = 42.665 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 MAR CCD 130 mm 2002-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.78 25 96.2 0.048 32.42 7444 7161 0.013
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) 1.78 1.81 78.8 0.375 282
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 1BY2 1.78 23.7 7155 7155 903 100 0.167 0.161 0.1589 0.21 0.2111 RANDOM 19.731
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] -0.87 0.63 0.79 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.782 r_dihedral_angle_4_deg 12.119 r_dihedral_angle_3_deg 11.671 r_dihedral_angle_1_deg 6.941 r_scangle_it 3.225 r_scbond_it 2.25 r_angle_refined_deg 1.345 r_mcangle_it 1.307 r_mcbond_it 0.813 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.782 r_dihedral_angle_4_deg 12.119 r_dihedral_angle_3_deg 11.671 r_dihedral_angle_1_deg 6.941 r_scangle_it 3.225 r_scbond_it 2.25 r_angle_refined_deg 1.345 r_mcangle_it 1.307 r_mcbond_it 0.813 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.197 r_nbd_refined 0.186 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 789 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection