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Crystal structure of the D76N Beta-2 Microglobulin mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 18-20% PEG 4000, 20% glycerol, 0.2M ammonium acetate, 0.1 M MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.91 35.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.22 α = 90 b = 28.42 β = 126.54 c = 52.26 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 110 CCD ADSC QUANTUM 4 Toroidal Zerodur mirror 2011-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.4 18.8 98.4 0.066 0.066 10.1 3.1 17632 14.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 98.9 0.375 0.375 2.9 3.3 2542
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 (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 1LDS 1.4 18.8 16709 892 97.89 0.13275 0.12995 0.1393 0.18616 0.192 RANDOM 14.763
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] 0.06 -0.02 -0.09 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.938 r_dihedral_angle_4_deg 25.519 r_dihedral_angle_3_deg 13.541 r_scangle_it 7.949 r_dihedral_angle_1_deg 7.046 r_scbond_it 5.749 r_mcangle_it 5.615 r_mcbond_it 4.359 r_rigid_bond_restr 2.564 r_angle_refined_deg 2.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.938 r_dihedral_angle_4_deg 25.519 r_dihedral_angle_3_deg 13.541 r_scangle_it 7.949 r_dihedral_angle_1_deg 7.046 r_scbond_it 5.749 r_mcangle_it 5.615 r_mcbond_it 4.359 r_rigid_bond_restr 2.564 r_angle_refined_deg 2.048 r_mcbond_other 1.672 r_angle_other_deg 0.993 r_chiral_restr 0.15 r_bond_refined_d 0.027 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 837 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 12
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling