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The Crystal Structure of human beta2-microglobulin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LDS PDB entry 1LDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 288 20% PEG4000, 25% glycerol, 0.2M ammonium acetate, 0.1M sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.2 44.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.649 α = 90 b = 28.869 β = 121.66 c = 54.756 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 IMAGE PLATE RIGAKU RAXIS VII 2005-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 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 1.7 37.96 97.3 0.069 8.1 3.5 11279 18.42
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) 1.7 1.79 87.1 0.412 2.4 2.8 1454
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1LDS 1.7 26.45 10740 10740 538 96.92 0.20833 0.20833 0.20705 0.23339 0.2197 RANDOM 16.708
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] -0.41 0.08 0.16 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.279 r_dihedral_angle_4_deg 20.634 r_dihedral_angle_3_deg 12.429 r_dihedral_angle_1_deg 6.76 r_scangle_it 4.445 r_scbond_it 2.731 r_mcangle_it 1.631 r_angle_refined_deg 1.448 r_mcbond_it 0.877 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.279 r_dihedral_angle_4_deg 20.634 r_dihedral_angle_3_deg 12.429 r_dihedral_angle_1_deg 6.76 r_scangle_it 4.445 r_scbond_it 2.731 r_mcangle_it 1.631 r_angle_refined_deg 1.448 r_mcbond_it 0.877 r_nbtor_refined 0.301 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.133 r_metal_ion_refined 0.124 r_chiral_restr 0.105 r_symmetry_hbond_refined 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 820 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing