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Crystal structure of a putative uncharacterized protein from Mycobacterium marinum bound to adenosine 5'-monophosphate AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QUA PDB ENTRY 3QUA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 289 MymaA.00620.b.A1 PW29922 at 27.2 mg/mL against JCSG+ screen condition C1, 0.2 M NaCl, 0.1 M phosphate/citrate pH 4.2, 20% PEG 8000 with 25% ethylene glycol as cryo-protection reagent, crystal tracking ID 218867c1, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.71 54.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.24 α = 106.7 b = 80.12 β = 90.13 c = 85.69 γ = 98.81
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 ADSC QUANTUM 315r 2011-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
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 2.5 50 90.4 0.057 11.16 1.8 58548 52931 -3
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 2.5 2.56 94.8 0.34 2.2 1.7
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 3QUA 2.5 50 50303 2622 90.5 0.24468 0.24249 0.2519 0.28752 0.2633 RANDOM 34.994
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] -1.49 -1.5 -1.07 1.43 -0.76 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.381 r_dihedral_angle_4_deg 19.571 r_dihedral_angle_3_deg 16.529 r_dihedral_angle_1_deg 5.204 r_scangle_it 1.682 r_angle_refined_deg 1.253 r_scbond_it 0.998 r_mcangle_it 0.923 r_mcbond_it 0.495 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.381 r_dihedral_angle_4_deg 19.571 r_dihedral_angle_3_deg 16.529 r_dihedral_angle_1_deg 5.204 r_scangle_it 1.682 r_angle_refined_deg 1.253 r_scbond_it 0.998 r_mcangle_it 0.923 r_mcbond_it 0.495 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10435 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 184
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction