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EGF Domains 1,2,5 of human EMR2, a 7-TM immune system molecule, in complex with calcium.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BOU PDB ENTRY 2BOU (BARIUM COMPLEX OF THE SAME PROTEIN)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1-0.175 M CALCIUM ACETATE, 12-16% W/V PEG 8000, 0.1 M NA CACODYLATE BUFFER PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.8 56.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.845 α = 90 b = 61.377 β = 84.1 c = 35.584 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 ADSC CCD 2002-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.6 29.5 99.2 0.08 6.1 3.3 10840 -4.823
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 2.6 2.74 99.4 0.41 2.2 3.4
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 (All) 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 2BOU (BARIUM COMPLEX OF THE SAME PROTEIN) 2.6 29.54 10174 10714 516 0.239 0.239 0.238 0.2517 0.26 0.2902 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation t_dihedral_angle_d 19.791 t_it 0.829 t_angle_deg 0.555 t_nbd 0.03 t_gen_planes 0.011 t_trig_c_planes 0.004 t_bond_d 0.003 t_incorr_chiral_ct t_pseud_angle t_omega_torsion
RMS Deviations Key Refinement Restraint Deviation t_dihedral_angle_d 19.791 t_it 0.829 t_angle_deg 0.555 t_nbd 0.03 t_gen_planes 0.011 t_trig_c_planes 0.004 t_bond_d 0.003 t_incorr_chiral_ct t_pseud_angle t_omega_torsion t_other_torsion t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2084 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 9
Software Software Software Name Purpose TNT refinement MOSFLM data reduction SCALA data scaling MOLREP phasing