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Crystal structure of YidC from Bacillus halodurans (form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other In-house Hg-phased model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 lipidic qubic phase 6 293 28-32% PEG500DME, 2. mM CdCl2, 100mM Na-(CH3)2AsO2, pH 6.0, lipidic qubic phase, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.76 55.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.926 α = 90 b = 60.631 β = 100.35 c = 58.903 γ = 90
Symmetry Space Group P 1 21 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 CCD RAYONIX MX225HE 2012-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 50 91 0.068 15.2 2.6 10889 42.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 85.6 0.318 1.9 511
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SeM-substituted protein structure 2.403 28.297 1.55 10879 544 90.69 0.2429 0.2421 0.2382 0.2587 0.2541 RANDOM 65.6209
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] -13.4163 -3.719 12.0963 1.32
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.07 f_angle_d 0.714 f_chiral_restr 0.046 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1601 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 61
Software Software Software Name Purpose SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction BSS data collection HKL-2000 data reduction PHENIX phasing