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Crystal structure of the ectodomain of the MlaD protein from Escherichia coli in the resting state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HPZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 293 0.01 M nickel(II) chloride hexahydrate, 0.1 M tris pH 8.5, 20% (w/v) PEG monoethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 2.14 42.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.28 α = 90 b = 64.28 β = 90 c = 231.06 γ = 90
Symmetry Space Group P 41 21 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 2019-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 3.2 77.02 99.8 0.166 0.175 0.053 0.994 9.6 10 8680
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 3.2 3.42 100 0.552 0.582 0.177 0.934 10.2
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 3.2 61.93 8175 442 99.66 0.21008 0.20644 0.2091 0.27543 0.2637 RANDOM 70.249
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] 1.99 1.99 -3.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.301 r_dihedral_angle_3_deg 20.208 r_dihedral_angle_4_deg 16.092 r_dihedral_angle_1_deg 8.027 r_long_range_B_refined 7.325 r_long_range_B_other 7.3 r_scangle_other 4.661 r_mcangle_it 4.387 r_mcangle_other 4.386 r_scbond_it 2.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.301 r_dihedral_angle_3_deg 20.208 r_dihedral_angle_4_deg 16.092 r_dihedral_angle_1_deg 8.027 r_long_range_B_refined 7.325 r_long_range_B_other 7.3 r_scangle_other 4.661 r_mcangle_it 4.387 r_mcangle_other 4.386 r_scbond_it 2.772 r_scbond_other 2.771 r_mcbond_it 2.609 r_mcbond_other 2.609 r_angle_refined_deg 1.812 r_angle_other_deg 1.217 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 2645 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms
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