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The Crystal Structure of human beta2-microglobulin, L39W W60F W95F Mutant
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 15% 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 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.423 α = 90 b = 28.776 β = 123.56 c = 57.241 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 2005-06-24 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 2.1 47.673 100 0.076 8.2 3.5 6345 6343 3 26.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.21 100 0.315 3.5 927
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1LDS 2.1 47.67 6047 294 99.94 0.21802 0.21802 0.21571 0.2131 0.26543 0.2715 RANDOM 25.258
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] -1.3 0.59 0.03 1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.895 r_dihedral_angle_3_deg 17.935 r_dihedral_angle_4_deg 14.189 r_dihedral_angle_1_deg 6.741 r_scangle_it 2.996 r_scbond_it 1.848 r_mcangle_it 1.518 r_angle_refined_deg 1.301 r_mcbond_it 0.813 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.895 r_dihedral_angle_3_deg 17.935 r_dihedral_angle_4_deg 14.189 r_dihedral_angle_1_deg 6.741 r_scangle_it 2.996 r_scbond_it 1.848 r_mcangle_it 1.518 r_angle_refined_deg 1.301 r_mcbond_it 0.813 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.155 r_metal_ion_refined 0.115 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 804 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing