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Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RM4 PDB ENTRY 1RM4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 2.0-2.5 M ammonium sulfate, 0.1 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.52 65.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.147 α = 90 b = 215.687 β = 102.52 c = 81.469 γ = 90
Symmetry Space Group C 1 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 ADSC QUANTUM 4 mirrors 2003-05-03 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4 mirrors 2003-05-03 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD MAR CCD 165 mm mirrors 2003-10-18 M SINGLE WAVELENGTH 1,2,3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2 2 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2 3 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.000 ELETTRA 5.2R
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 1,2,3 3.6 91 99.9 0.359 0.359 4.5 13.4 36736 36699 3 -3 15.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2,3 3.6 3.73 99.3 0.694 0.694 1.5 3647
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 (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 1RM4 3.6 90.86 36736 36271 1802 99.9 0.261 0.261 0.2474 0.292 0.2765 RANDOM 30.9
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] 6.13 -10.38 7 -13.12
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.6 c_improper_angle_d 5.21 c_scangle_it 2.13 c_mcangle_it 1.98 c_angle_deg 1.9 c_scbond_it 1.25 c_mcbond_it 1.11 c_bond_d 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15477 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 363
Software Software Software Name Purpose CNS refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing