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Crystal structure of the MlaD domain of the MlaD protein from Escherichia coli (Form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UW8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5 293 1.8 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic pH 5.0
Crystal Properties Matthews coefficient Solvent content 1.82 32.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.28 α = 90 b = 107.29 β = 90 c = 117.92 γ = 90
Symmetry Space Group I 2 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 IMAGE PLATE RIGAKU RAXIS IV++ VariMax HF 2020-01-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU R-AXIS IV 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 79.36 99.9 0.082 0.088 0.032 0.993 13.6 7.9 17387
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 0.595 0.636 0.223 0.936 7.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.3 79.36 16498 859 99.77 0.22746 0.22505 0.2294 0.2725 0.2678 RANDOM 54.142
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] 5.78 -2.94 -2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.965 r_dihedral_angle_4_deg 25.439 r_dihedral_angle_3_deg 19.623 r_dihedral_angle_1_deg 8.773 r_long_range_B_refined 7.234 r_long_range_B_other 7.232 r_scangle_other 4.616 r_mcangle_it 4.398 r_mcangle_other 4.398 r_scbond_it 2.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.965 r_dihedral_angle_4_deg 25.439 r_dihedral_angle_3_deg 19.623 r_dihedral_angle_1_deg 8.773 r_long_range_B_refined 7.234 r_long_range_B_other 7.232 r_scangle_other 4.616 r_mcangle_it 4.398 r_mcangle_other 4.398 r_scbond_it 2.826 r_scbond_other 2.825 r_mcbond_it 2.659 r_mcbond_other 2.641 r_angle_refined_deg 1.867 r_angle_other_deg 1.289 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 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 2400 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 7
Software Software Software Name Purpose HKL-3000 data collection MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction