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Apo Glyceraldehyde 3-phosphate Dehydrogenase (GapA) from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GD1 monomer with ligands removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 300 17% w/v PEG8000, 100mM Hepes, 12mg/ml protein
Crystal Properties Matthews coefficient Solvent content 2.61 52.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.16 α = 90 b = 100.617 β = 93.696 c = 97.792 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 4r 2003-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.74 95.4 99 0.161 19 2.1 147140
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 1.74 1.82 99 0.534 2.2 2.1
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 1.74 95.346 147140 7374 99.053 0.152 0.1498 0.1635 0.1995 0.2077 27.35
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] 1.598 3.3 -0.82 -1.194
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.766 r_lrange_other 19.002 r_dihedral_angle_6_deg 15.892 r_scangle_it 12.955 r_scangle_other 12.954 r_dihedral_angle_3_deg 12.263 r_mcangle_it 10.251 r_mcangle_other 10.251 r_scbond_it 8.868 r_scbond_other 8.86
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.766 r_lrange_other 19.002 r_dihedral_angle_6_deg 15.892 r_scangle_it 12.955 r_scangle_other 12.954 r_dihedral_angle_3_deg 12.263 r_mcangle_it 10.251 r_mcangle_other 10.251 r_scbond_it 8.868 r_scbond_other 8.86 r_dihedral_angle_2_deg 7.696 r_mcbond_it 7.273 r_mcbond_other 7.271 r_dihedral_angle_1_deg 7.072 r_rigid_bond_restr 4.269 r_angle_refined_deg 1.642 r_angle_other_deg 0.57 r_nbd_refined 0.217 r_symmetry_nbd_other 0.206 r_nbd_other 0.187 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_refined 0.154 r_symmetry_nbd_refined 0.145 r_metal_ion_refined 0.1 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.081 r_symmetry_xyhbond_nbd_other 0.047 r_bond_refined_d 0.008 r_chiral_restr_other 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9706 Nucleic Acid Atoms Solvent Atoms 1006 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALEPACK data scaling PHASER phasing