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Crystal structure of the MlaD domain of the MlaD protein from Escherichia coli (Form II)
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 5 293 0.2 M magnesium chloride hexahydrate, 0.1 M sodium citrate tribasic dihyrate pH 5.0, 10% (w/v) PEG 20000
Crystal Properties Matthews coefficient Solvent content 1.81 31.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.42 α = 90 b = 106.95 β = 90 c = 117.12 γ = 90
Symmetry Space Group P 21 2 21
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 2020-01-07 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 2.7 79.1 100 0.148 0.157 0.052 0.996 12.6 8.8 21557
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 2.7 2.83 100 0.612 0.65 0.216 0.943 8.9
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 2.7 78.98 20487 1037 99.99 0.20686 0.20415 0.2065 0.26108 0.2608 RANDOM 42.567
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] 3.88 -2.06 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.386 r_dihedral_angle_3_deg 21.152 r_dihedral_angle_4_deg 20.096 r_dihedral_angle_1_deg 8.584 r_long_range_B_refined 6.135 r_long_range_B_other 6.106 r_scangle_other 3.737 r_mcangle_it 3.498 r_mcangle_other 3.498 r_scbond_it 2.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.386 r_dihedral_angle_3_deg 21.152 r_dihedral_angle_4_deg 20.096 r_dihedral_angle_1_deg 8.584 r_long_range_B_refined 6.135 r_long_range_B_other 6.106 r_scangle_other 3.737 r_mcangle_it 3.498 r_mcangle_other 3.498 r_scbond_it 2.174 r_scbond_other 2.173 r_mcbond_other 1.999 r_mcbond_it 1.998 r_angle_refined_deg 1.827 r_angle_other_deg 1.25 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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 4824 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 4
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