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Crystal structure of D-erythrulose 4-phosphate dehydrogenase from Brucella melitensis, solved by iodide SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 EmeraldBio JCSG screen, a3: 20% PEG 3350, 200mM ammonium citrate; BrmeA.18135.a.A1.PS01411 at 20mg/ml; crystal from tray 235328a3 incubated with 500mM NaI, 20% EG in 2 steps, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.5 α = 90 b = 103.5 β = 90 c = 256.54 γ = 120
Symmetry Space Group P 62 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 CCD RIGAKU SATURN 944+ 2012-07-06 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD RIGAKU SATURN 944+ 2012-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418 2 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.95 50 99.7 0.09 0.09 24.13 17.2 60098 59958 -3 22.275
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 1.95 2 97.6 0.257 6.65
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1.95 44.86 60098 56896 3029 99.75 0.1944 0.1927 0.199 0.2257 0.2281 RANDOM 17.7039
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] 0.25 0.25 0.25 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.343 r_dihedral_angle_4_deg 18.551 r_dihedral_angle_3_deg 13.032 r_dihedral_angle_1_deg 6.019 r_angle_refined_deg 1.366 r_angle_other_deg 0.814 r_mcangle_it 0.752 r_mcbond_it 0.442 r_mcbond_other 0.441 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.343 r_dihedral_angle_4_deg 18.551 r_dihedral_angle_3_deg 13.032 r_dihedral_angle_1_deg 6.019 r_angle_refined_deg 1.366 r_angle_other_deg 0.814 r_mcangle_it 0.752 r_mcbond_it 0.442 r_mcbond_other 0.441 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4852 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 26
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction JDirector data collection XDS data reduction