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Crystal structure of glyceraldehyde-3-phosphate dehydrogenase GapN from Methanocaldococcus jannaschii DSM 2661 complexed with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PQA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 35% MPD, 0.1M acetate, 4.5, 2 mM NADPH, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.243 α = 90 b = 77.384 β = 118.29 c = 167.389 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 315 2011-02-11 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9791 NSLS X29A
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 50 99.7 0.116 6.6 5.4 93993
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 96.5 5 4547
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3PQA 2.2 19.96 93586 4688 99.59 0.1823 0.1794 0.1818 0.2385 0.2407 RANDOM 27.9527
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] 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.078 r_dihedral_angle_3_deg 15.649 r_dihedral_angle_4_deg 15.35 r_scbond_it 8.449 r_dihedral_angle_1_deg 6.078 r_mcangle_it 3.375 r_angle_refined_deg 1.264 r_scangle_it 0.829 r_mcbond_it 0.702 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.078 r_dihedral_angle_3_deg 15.649 r_dihedral_angle_4_deg 15.35 r_scbond_it 8.449 r_dihedral_angle_1_deg 6.078 r_mcangle_it 3.375 r_angle_refined_deg 1.264 r_scangle_it 0.829 r_mcbond_it 0.702 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14132 Nucleic Acid Atoms Solvent Atoms 610 Heterogen Atoms 124
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction