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Crystal structure of human glycerol-3-phosphate dehydrogenase 1-like protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X0V PDB entry 1X0V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 277 50% PEG 300, 0.2M Sodium chloride, 0.1M Sodium potassium phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4 69.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.1 α = 90 b = 139.1 β = 90 c = 109.62 γ = 120
Symmetry Space Group P 31 2 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 MARMOSAIC 225 mm CCD 2007-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.79887 SLS X10SA
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 2.51 50 99.7 0.061 19 7.5 42245 42245 67.6
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 2.51 2.66 98.5 0.621 3.39 7.5 6634
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1X0V 2.51 29.361 42226 42226 2127 99.63 0.177 0.177 0.175 0.1771 0.212 0.2045 RANDOM 28.714
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] 1.05 0.53 1.05 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.782 r_dihedral_angle_4_deg 19.987 r_dihedral_angle_3_deg 15.527 r_dihedral_angle_1_deg 5.338 r_scangle_it 1.924 r_angle_refined_deg 1.306 r_scbond_it 1.183 r_angle_other_deg 0.915 r_mcangle_it 0.708 r_mcbond_it 0.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.782 r_dihedral_angle_4_deg 19.987 r_dihedral_angle_3_deg 15.527 r_dihedral_angle_1_deg 5.338 r_scangle_it 1.924 r_angle_refined_deg 1.306 r_scbond_it 1.183 r_angle_other_deg 0.915 r_mcangle_it 0.708 r_mcbond_it 0.412 r_symmetry_vdw_other 0.255 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.191 r_nbd_other 0.178 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.143 r_symmetry_vdw_refined 0.112 r_nbtor_other 0.084 r_mcbond_other 0.072 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5155 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 104
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction XDS data scaling