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Crystal structure of wildtype MENT in the native conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H4S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 290 20% PEG-4000, 0.1M sodium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.04 39.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.203 α = 90 b = 74.022 β = 95.42 c = 57.505 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 IV 2004-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.7 40 97.1 0.185 4.4 3 10420
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) 1 2.7 2.8 95.8 0.571 2.4 2.9
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 (All) 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 2H4S 2.7 18.96 10379 501 97.28 0.209 0.205 0.209 0.282 0.2855 RANDOM 49.724
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] -0.01 -0.06 -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.264 r_dihedral_angle_3_deg 14.722 r_dihedral_angle_4_deg 12.849 r_dihedral_angle_1_deg 4.1 r_scangle_it 3.663 r_scbond_it 2.442 r_mcangle_it 1.786 r_angle_refined_deg 1.199 r_mcbond_it 0.987 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.264 r_dihedral_angle_3_deg 14.722 r_dihedral_angle_4_deg 12.849 r_dihedral_angle_1_deg 4.1 r_scangle_it 3.663 r_scbond_it 2.442 r_mcangle_it 1.786 r_angle_refined_deg 1.199 r_mcbond_it 0.987 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.276 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.189 r_symmetry_vdw_refined 0.178 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3026 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOLREP phasing