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MamM CTD E289D - Cadmium form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M (NH4)2SO4,
0.1M BIS-TRIS pH=6.5,
0.1M NaCl,
1.7mM CdCl2
Crystal Properties Matthews coefficient Solvent content 2.23 44.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.599 α = 90 b = 94.545 β = 91.76 c = 107.49 γ = 90
Symmetry Space Group I 1 2 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 PIXEL DECTRIS PILATUS 6M 2017-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 47.27 99.3 0.273 0.984 5.7 6.8 22985
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 97.5 0.639 1.7 6.9
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 (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 3W5X 2.7 47.27 21606 1140 98.26 0.25167 0.24964 0.2519 0.29043 0.2968 RANDOM 37.972
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] 1.58 -0.45 -2.25 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.895 r_dihedral_angle_4_deg 21.37 r_dihedral_angle_3_deg 18.674 r_dihedral_angle_1_deg 7.12 r_long_range_B_refined 3.925 r_long_range_B_other 3.925 r_mcangle_it 1.569 r_mcangle_other 1.569 r_scangle_other 1.536 r_scbond_it 1.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.895 r_dihedral_angle_4_deg 21.37 r_dihedral_angle_3_deg 18.674 r_dihedral_angle_1_deg 7.12 r_long_range_B_refined 3.925 r_long_range_B_other 3.925 r_mcangle_it 1.569 r_mcangle_other 1.569 r_scangle_other 1.536 r_scbond_it 1.423 r_scbond_other 1.423 r_angle_refined_deg 1.346 r_mcbond_it 0.9 r_mcbond_other 0.9 r_angle_other_deg 0.856 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4516 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing