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MamM CTD E289D - Manganese 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 0.2M LiSO4,
0.1M BIS-TRIS pH=5.5,
25% PEG 3350,
1.7 mM MnCl2
Crystal Properties Matthews coefficient Solvent content 2.17 43.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.261 α = 90 b = 78.261 β = 90 c = 175.495 γ = 120
Symmetry Space Group P 62 2 2
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 2017-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976247 ESRF ID29
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 2.09 44.28 99 0.081 1 18.5 17.6 19491
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 2.09 2.15 87.6 0.837 1.2 13.8 442
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 2.1 44.28 15614 805 84.39 0.21534 0.21405 0.2228 0.23924 0.2496 RANDOM 45.488
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] 0.05 0.03 0.05 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.339 r_dihedral_angle_3_deg 17.344 r_dihedral_angle_4_deg 13.68 r_dihedral_angle_1_deg 6.44 r_long_range_B_refined 6.329 r_long_range_B_other 6.325 r_scangle_other 3.944 r_mcangle_it 2.735 r_mcangle_other 2.734 r_scbond_it 2.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.339 r_dihedral_angle_3_deg 17.344 r_dihedral_angle_4_deg 13.68 r_dihedral_angle_1_deg 6.44 r_long_range_B_refined 6.329 r_long_range_B_other 6.325 r_scangle_other 3.944 r_mcangle_it 2.735 r_mcangle_other 2.734 r_scbond_it 2.474 r_scbond_other 2.435 r_angle_refined_deg 1.904 r_mcbond_it 1.761 r_mcbond_other 1.76 r_angle_other_deg 1.024 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1938 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing