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Crystal structure of grass carp Beta2-microglobulin
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 EVAPORATION 6.5 291 0.1M MES pH 6.5, 12% PEG 20000, 3%(v/v) ethanol, EVAPORATION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.52 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.74 α = 90 b = 40.601 β = 90 c = 71.094 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 35.56 6986
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1LDS 2.1 30 6095 309 92.25 0.19809 0.19548 0.25206 0.194 RANDOM 30.93
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] -0.09 -0.82 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.692 r_dihedral_angle_3_deg 16.142 r_dihedral_angle_1_deg 7.085 r_dihedral_angle_4_deg 5.913 r_scangle_it 3.197 r_scbond_it 1.983 r_mcangle_it 1.545 r_angle_refined_deg 1.389 r_mcbond_it 0.939 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.692 r_dihedral_angle_3_deg 16.142 r_dihedral_angle_1_deg 7.085 r_dihedral_angle_4_deg 5.913 r_scangle_it 3.197 r_scbond_it 1.983 r_mcangle_it 1.545 r_angle_refined_deg 1.389 r_mcbond_it 0.939 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.232 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.18 r_symmetry_vdw_refined 0.17 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 781 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement