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High resolution structure of the major periplasmic domain from the cell shape-determining filament MreC (monoclinic form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QF4 PDB entry 2QF4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 0.1M Sodium acetate pH 4.6, 0.2M Ammonium sulfate, 12.5% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.38 48.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.998 α = 90 b = 48.283 β = 115.32 c = 48.429 γ = 90
Symmetry Space Group C 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 IMAGE PLATE MAR scanner 300 mm plate 2006-06-15 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) R Sym I (Observed) 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 2.23 23.83 90.3 0.03 0.03 18.3 5.2 7873
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.23 2.33 76.4 0.123 0.123 6 5.1 966
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 PDB entry 2QF4 2.23 23.83 7870 365 92.72 0.197 0.194 0.1971 0.268 0.2703 RANDOM 20.21
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] 2.9 -1.19 -1.76 -2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.843 r_dihedral_angle_4_deg 22.352 r_dihedral_angle_3_deg 15.396 r_dihedral_angle_1_deg 6.329 r_scangle_it 2.393 r_scbond_it 1.541 r_angle_refined_deg 1.376 r_angle_other_deg 0.882 r_mcangle_it 0.867 r_mcbond_it 0.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.843 r_dihedral_angle_4_deg 22.352 r_dihedral_angle_3_deg 15.396 r_dihedral_angle_1_deg 6.329 r_scangle_it 2.393 r_scbond_it 1.541 r_angle_refined_deg 1.376 r_angle_other_deg 0.882 r_mcangle_it 0.867 r_mcbond_it 0.688 r_symmetry_vdw_other 0.254 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.195 r_nbd_other 0.19 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.155 r_symmetry_vdw_refined 0.145 r_mcbond_other 0.124 r_nbtor_other 0.086 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1161 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing