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Crystal structure of a M-loop deletion variant of MENT in the cleaved conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QLP PDB ENTRY 1QLP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 290 0.1M sodium acetate, 12-15% PEG 8000, pH 5.5-6.5, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.97 68.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.194 α = 90 b = 150.194 β = 90 c = 175.485 γ = 120
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 IV OSMIC MIRRORS 2003-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ELLIOTT GX-13 1.5148
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 2.1 105.4 99.3 0.062 20.7 3.4 44451 44451 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.18 94.6 0.587 2.4 2.7
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 1QLP 2.1 24.35 44118 44118 1782 99.29 0.189 0.189 0.188 0.2042 0.213 0.2268 RANDOM 32.052
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] -0.7 -0.35 -0.7 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.243 r_dihedral_angle_4_deg 13.132 r_dihedral_angle_3_deg 11.186 r_dihedral_angle_1_deg 5.645 r_scangle_it 2.838 r_scbond_it 1.881 r_mcangle_it 1.376 r_angle_refined_deg 0.874 r_mcbond_it 0.862 r_angle_other_deg 0.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.243 r_dihedral_angle_4_deg 13.132 r_dihedral_angle_3_deg 11.186 r_dihedral_angle_1_deg 5.645 r_scangle_it 2.838 r_scbond_it 1.881 r_mcangle_it 1.376 r_angle_refined_deg 0.874 r_mcbond_it 0.862 r_angle_other_deg 0.662 r_symmetry_hbond_refined 0.202 r_nbd_refined 0.177 r_nbtor_refined 0.172 r_nbd_other 0.155 r_symmetry_vdw_other 0.147 r_symmetry_vdw_refined 0.135 r_xyhbond_nbd_refined 0.126 r_mcbond_other 0.123 r_nbtor_other 0.077 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3093 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction SCALEPACK data scaling AMoRE phasing