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Crystal structure of glycerol-3-phosphate dehydrogenase (TM0378) from THERMOTOGA MARITIMA at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 8 277 0.2M MgCl2, 35.0% MPD, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.03 39.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.09 α = 90 b = 67.451 β = 113.67 c = 75.597 γ = 90
Symmetry Space Group P 1 21 1
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 315 2005-02-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.891940,0.979245 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 29.81 98.4 0.083 7.2 3.5 40008
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 98.5 0.558 1.3 3.5
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 (All) 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 29.81 37984 2024 98.34 0.168 0.16824 0.166 0.1764 0.211 0.2212 RANDOM 29.469
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] 3.37 0.87 -0.29 -2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.88 r_dihedral_angle_4_deg 20.557 r_dihedral_angle_3_deg 15.171 r_dihedral_angle_1_deg 5.536 r_scangle_it 3.441 r_scbond_it 2.346 r_angle_refined_deg 1.621 r_mcangle_it 1.284 r_mcbond_it 1.052 r_angle_other_deg 1.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.88 r_dihedral_angle_4_deg 20.557 r_dihedral_angle_3_deg 15.171 r_dihedral_angle_1_deg 5.536 r_scangle_it 3.441 r_scbond_it 2.346 r_angle_refined_deg 1.621 r_mcangle_it 1.284 r_mcbond_it 1.052 r_angle_other_deg 1.032 r_symmetry_vdw_other 0.233 r_nbd_refined 0.212 r_mcbond_other 0.209 r_nbd_other 0.182 r_nbtor_refined 0.18 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.157 r_chiral_restr 0.085 r_nbtor_other 0.085 r_bond_refined_d 0.017 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 4812 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling SOLVE phasing