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Crystal structure of NAD-dependent malic enzyme (TM0542) from Thermotoga maritima at 2.61 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 277 0.025M Citric Acid, 0.075M Citrate_Na3, 6.00% NP_Peg 6000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K 2 VAPOR DIFFUSION,SITTING DROP,NANODROP 277 0.025M Citric Acid, 0.075M Citrate_Na3, 6.00% NP_Peg 6000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.85 56.87 3.12 60.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.963 α = 90 b = 143.963 β = 90 c = 163.428 γ = 120
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 2003-07-25 M SINGLE WAVELENGTH 2 1 x-ray 100 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1 2 SYNCHROTRON ALS BEAMLINE 8.3.1 1.019943, 0.979762, 0.979619 ALS 8.3.1
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 2.6 47.12 98.84 0.054 16.77 3.26 57871 74.19
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 2.6 2.69 96.26 0.551 1.84 2.86 5591
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.61 47.12 55267 2333 98.53 0.1938 0.19189 0.2005 0.23929 0.2339 RANDOM 61.902
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] 1.1 0.55 1.1 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.556 r_dihedral_angle_3_deg 17.945 r_dihedral_angle_4_deg 17.668 r_scangle_it 8.133 r_dihedral_angle_1_deg 6.65 r_scbond_it 5.8 r_mcangle_it 2.64 r_angle_refined_deg 1.658 r_mcbond_it 1.521 r_angle_other_deg 0.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.556 r_dihedral_angle_3_deg 17.945 r_dihedral_angle_4_deg 17.668 r_scangle_it 8.133 r_dihedral_angle_1_deg 6.65 r_scbond_it 5.8 r_mcangle_it 2.64 r_angle_refined_deg 1.658 r_mcbond_it 1.521 r_angle_other_deg 0.933 r_mcbond_other 0.492 r_symmetry_vdw_refined 0.4 r_symmetry_vdw_other 0.274 r_nbd_refined 0.236 r_nbtor_refined 0.189 r_nbd_other 0.179 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.096 r_symmetry_hbond_refined 0.094 r_nbtor_other 0.091 r_xyhbond_nbd_other 0.065 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11096 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction MOSFLM data reduction SCALEPACK data scaling SOLVE phasing SHARP phasing REFMAC refinement