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Glyceraldehyde 3-phosphate Dehydrogenase (GapA) from Helicobacter pylori in Complex with NAPD (Holo)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GD1 one monomer (O chain +NAD)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 293 100mM Tris, 36% v/v methanol, 1mM NADP
Crystal Properties Matthews coefficient Solvent content 2.51 50.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.938 α = 90 b = 116.938 β = 90 c = 95.474 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 QUANTUM 4r 2007-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 2.6 69.5 96.8 0.045 17.9 3.6 43460
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 2.6 2.74 88.3 0.193 5.7 2.6
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.6 44.774 43438 2077 96.826 0.178 0.1746 0.1802 0.2414 0.2483 55.246
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] 0.809 0.404 0.809 -2.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.805 r_dihedral_angle_3_deg 13.487 r_dihedral_angle_2_deg 9.769 r_lrange_other 8.257 r_lrange_it 8.256 r_dihedral_angle_1_deg 7.166 r_scangle_it 6.603 r_scangle_other 6.603 r_mcangle_it 5.978 r_mcangle_other 5.978
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.805 r_dihedral_angle_3_deg 13.487 r_dihedral_angle_2_deg 9.769 r_lrange_other 8.257 r_lrange_it 8.256 r_dihedral_angle_1_deg 7.166 r_scangle_it 6.603 r_scangle_other 6.603 r_mcangle_it 5.978 r_mcangle_other 5.978 r_scbond_it 4.49 r_scbond_other 4.485 r_mcbond_it 4.236 r_mcbond_other 4.233 r_dihedral_angle_other_2_deg 2.444 r_angle_refined_deg 1.524 r_angle_other_deg 0.492 r_nbd_refined 0.22 r_symmetry_nbd_other 0.204 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_refined 0.177 r_nbtor_refined 0.17 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.134 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.066 r_symmetry_xyhbond_nbd_other 0.048 r_bond_refined_d 0.007 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 10357 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing