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Crystal structure of the human beta-2 microglobulin mutant W60G
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PY4 PDB ENTRY 1PY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1M MES, PEG 4000, Ammonium acetate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.678 α = 90 b = 29.014 β = 125.26 c = 59.16 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 neutron 110 CCD MARMOSAIC 225 mm CCD 2007-02-06 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 19.2 93.2 0.068 14.9 2.9 9273 9273 13.3
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) 1 1.8 1.9 95.9 0.112 8 2.8 1375
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1PY4 1.8 19.16 2 9273 9273 489 93.2 0.17594 0.17382 0.2117 0.21424 0.2408 RANDOM 7.56
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] -0.57 -0.21 0.03 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.015 r_dihedral_angle_3_deg 13.617 r_dihedral_angle_4_deg 12.118 r_dihedral_angle_1_deg 6.118 r_scangle_it 1.512 r_angle_refined_deg 1.241 r_scbond_it 1.09 r_angle_other_deg 0.807 r_mcangle_it 0.614 r_mcbond_it 0.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.015 r_dihedral_angle_3_deg 13.617 r_dihedral_angle_4_deg 12.118 r_dihedral_angle_1_deg 6.118 r_scangle_it 1.512 r_angle_refined_deg 1.241 r_scbond_it 1.09 r_angle_other_deg 0.807 r_mcangle_it 0.614 r_mcbond_it 0.487 r_symmetry_vdw_refined 0.31 r_symmetry_vdw_other 0.244 r_nbd_refined 0.233 r_nbd_other 0.196 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.172 r_symmetry_hbond_refined 0.141 r_mcbond_other 0.096 r_chiral_restr 0.085 r_nbtor_other 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 827 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling MOLREP phasing