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Biochemical and Structural Analysis of the Molybdenum Cofactor Biosynthesis protein MobA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E5K PDB ENTRY 1E5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 12 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 20%(V/V) ISOPROPANOL 2% (W/V) PEG 1500, IN 100 MM CITRIC ACID BROUGHT TO PH 5.5 WITH NAOH. CRYSTALS GROW AT 4 DEG. C AND TAKE UP TO 8 WEEKS TO REACH FULL SIZE.
Crystal Properties Matthews coefficient Solvent content 1.93 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.224 α = 90 b = 41.752 β = 90 c = 54.514 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 MARRESEARCH 2000-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.5 SRS PX9.5
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 1.65 40 98.7 0.062 20.9 3.3 21218 -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 1.65 1.69 88 0.266 2.9
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1E5K 1.65 54.23 20152 1065 98.7 0.179 0.217 0.2238 RANDOM 17.82
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] 0.05 0.47 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.599 r_scangle_it 4.827 r_scbond_it 3.133 r_mcangle_it 2.262 r_angle_refined_deg 1.879 r_mcbond_it 1.292 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.189 r_xyhbond_nbd_refined 0.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.599 r_scangle_it 4.827 r_scbond_it 3.133 r_mcangle_it 2.262 r_angle_refined_deg 1.879 r_mcbond_it 1.292 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.189 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1431 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling