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The high resolution crystal structure of beta2-microglobulin under physiological conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D4F PDB ENTRY 2D4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 288 25% PEG 4000, 25% Glycerol, 0.06M ammoniumacetate, 0.1M MOPS, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.19 43.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.644 α = 90 b = 28.907 β = 121.59 c = 54.397 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 90 CCD Bruker DIP-6040 2005-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.65 SPring-8 BL44XU
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 1.13 26.63 100 0.051 12.4 3.8 38852 38852 9.459
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) 1.13 1.19 100 0.332 4 3.7 5630
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 2D4F 1.13 26.49 38852 36904 1948 99.98 0.18436 0.1838 0.193 0.19486 0.2008 RANDOM 11.113
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] -0.38 -0.03 0.23 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.353 r_dihedral_angle_4_deg 21.752 r_dihedral_angle_3_deg 11.286 r_dihedral_angle_1_deg 6.909 r_sphericity_free 2.98 r_scangle_it 2.541 r_rigid_bond_restr 2.029 r_scbond_it 1.978 r_sphericity_bonded 1.845 r_mcangle_it 1.369
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.353 r_dihedral_angle_4_deg 21.752 r_dihedral_angle_3_deg 11.286 r_dihedral_angle_1_deg 6.909 r_sphericity_free 2.98 r_scangle_it 2.541 r_rigid_bond_restr 2.029 r_scbond_it 1.978 r_sphericity_bonded 1.845 r_mcangle_it 1.369 r_angle_refined_deg 1.227 r_mcbond_it 1.187 r_angle_other_deg 0.744 r_mcbond_other 0.302 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.2 r_nbd_other 0.195 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.15 r_symmetry_vdw_other 0.142 r_xyhbond_nbd_refined 0.139 r_nbtor_other 0.084 r_chiral_restr 0.08 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 828 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling