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Crystal structure of a putative uncharacterized protein from Mycobacterium smegmatis, an ortholog of Rv0543c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OL3 PDB entry 3OL3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 52.57 mg/mL MysmA,17112.a.A1 PS00688 against PACT screen condition F12, 0.2 M sodium malonate, 0.1 M BisTris Propane pH 6.5, 20% PEG 3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 217010f12, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.5 50.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.21 α = 90 b = 72.69 β = 90 c = 45.13 γ = 90
Symmetry Space Group P 21 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 CCD RIGAKU SATURN 944+ VariMax HF 2010-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 50 98 0.048 19.25 3.2 16421 16088 -3 29.089
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 2.05 86.5 0.285 3.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3OL3 2 50 16005 803 97.46 0.204 0.202 0.2422 0.2158 RANDOM 37.8828
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] -0.02 0.4 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.226 r_dihedral_angle_4_deg 15.497 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_1_deg 4.241 r_scangle_it 3.872 r_scbond_it 2.365 r_mcangle_it 1.658 r_angle_refined_deg 1.237 r_mcbond_it 0.908 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.226 r_dihedral_angle_4_deg 15.497 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_1_deg 4.241 r_scangle_it 3.872 r_scbond_it 2.365 r_mcangle_it 1.658 r_angle_refined_deg 1.237 r_mcbond_it 0.908 r_chiral_restr 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1475 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction