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Crystal structure of a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis str. 168 at 2.62 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 50.0% polyethylene glycol 200, 0.1M TRIS pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.77 67.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.653 α = 90 b = 98.653 β = 90 c = 195.018 γ = 120
Symmetry Space Group P 65 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 PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2014-06-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97971,0.91837,0.97926 SSRL BL11-1
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 2.62 49.327 99.8 0.09 22.88 17632 -3 84.781
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.62 2.71 99.9 0.023 2.396 1.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.62 49.327 17574 889 99.87 0.2147 0.2135 0.2389 0.2276 RANDOM 89.4081
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] -13.4645 -13.4645 26.9289
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.12 t_omega_torsion 3.08 t_angle_deg 1.21 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.12 t_omega_torsion 3.08 t_angle_deg 1.21 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2485 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 39
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling BUSTER-TNT refinement XDS data reduction SHELXD phasing BUSTER refinement