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Crystal structure of Ig-like C2-type 2 domain of the human Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U2H PDB entries 1U2H, 2AW2, 1CS6 experimental model PDB 2AW2 PDB entries 1U2H, 2AW2, 1CS6 experimental model PDB 1CS6 PDB entries 1U2H, 2AW2, 1CS6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1:1 volume ratio of protein solution (50 mg/mL) and reservoir solution (30% PEG MME 550, 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.88 34.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.944 α = 66.5 b = 43.64 β = 90 c = 49.595 γ = 90.02
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 Rh coated Si monochromatic mirrors 2007-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.91790 CHESS F1
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 1.15 25 94.6 0.06 22 5.1 103829 103829 -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) 1.15 1.19 91.8 0.651 2.48 3.7 10043
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 PDB entries 1U2H, 2AW2, 1CS6 1.15 25 98073 5145 94.57 0.17882 0.17708 0.1833 0.21182 0.2183 RANDOM 19.976
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] 0.93 0.17 -0.19 -0.67 0.63 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.076 r_dihedral_angle_4_deg 23.895 r_dihedral_angle_3_deg 13.739 r_sphericity_free 9.706 r_dihedral_angle_1_deg 7.17 r_sphericity_bonded 6.543 r_scangle_it 5.09 r_scbond_it 4.006 r_mcangle_it 3.337 r_rigid_bond_restr 2.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.076 r_dihedral_angle_4_deg 23.895 r_dihedral_angle_3_deg 13.739 r_sphericity_free 9.706 r_dihedral_angle_1_deg 7.17 r_sphericity_bonded 6.543 r_scangle_it 5.09 r_scbond_it 4.006 r_mcangle_it 3.337 r_rigid_bond_restr 2.792 r_mcbond_it 2.535 r_angle_refined_deg 1.83 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.226 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.128 r_bond_refined_d 0.017 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3040 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing