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Crystal structure of L3MBTL1 protein in complex with MES
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PQW PDB entry 2PQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 300 4% PEG 4000, 0.1 M Sodium acetate, 0.1 M MES pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.76 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.548 α = 90 b = 108.784 β = 90.91 c = 90.348 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS varimax 2006-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 1.54000
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 2 90.17 99.9 0.088 3.6 82054 82054
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 (All) 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 2PQW 2 90.17 78050 78050 4116 99.65 0.19718 0.19718 0.19487 0.1904 0.24127 0.2348 RANDOM 26.048
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] 0.8 0.15 0.08 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.007 r_dihedral_angle_4_deg 21.35 r_dihedral_angle_3_deg 14.916 r_dihedral_angle_1_deg 7.118 r_scangle_it 3.562 r_scbond_it 2.508 r_angle_refined_deg 1.679 r_mcangle_it 1.481 r_mcbond_it 1.018 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.007 r_dihedral_angle_4_deg 21.35 r_dihedral_angle_3_deg 14.916 r_dihedral_angle_1_deg 7.118 r_scangle_it 3.562 r_scbond_it 2.508 r_angle_refined_deg 1.679 r_mcangle_it 1.481 r_mcbond_it 1.018 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.232 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.119 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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 7575 Nucleic Acid Atoms Solvent Atoms 739 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing