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Glyceraldehyde 3-phosphate dehydrogenase from Campylobacter jejeuni - ADP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 295 0.1M Sodium Acetate, 2.0 M Ammonium Sulfate,
Crystal Properties Matthews coefficient Solvent content 3.16 61.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.25 α = 90 b = 90.25 β = 90 c = 223.39 γ = 90
Symmetry Space Group I 41 2 2
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 RIGAKU varimax HF 2013-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.05 83.67 91.3 0.13 9.9 10.9 29280
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 2.05 2.11 94.9 0.32 6.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7BEW 2.054 30.105 29252 1437 99.898 0.156 0.1546 0.1671 0.1905 0.1997 random 17.297
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] -0.007 -0.007 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.285 r_dihedral_angle_4_deg 18.219 r_dihedral_angle_3_deg 12.756 r_dihedral_angle_1_deg 7.513 r_lrange_it 5.817 r_lrange_other 5.774 r_scangle_it 4.376 r_scangle_other 4.375 r_scbond_it 2.981 r_scbond_other 2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.285 r_dihedral_angle_4_deg 18.219 r_dihedral_angle_3_deg 12.756 r_dihedral_angle_1_deg 7.513 r_lrange_it 5.817 r_lrange_other 5.774 r_scangle_it 4.376 r_scangle_other 4.375 r_scbond_it 2.981 r_scbond_other 2.98 r_mcangle_other 2.494 r_mcangle_it 2.493 r_angle_refined_deg 1.709 r_mcbond_it 1.619 r_mcbond_other 1.607 r_angle_other_deg 1.422 r_nbd_refined 0.203 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_refined 0.187 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_other 0.163 r_xyhbond_nbd_refined 0.153 r_nbd_other 0.144 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2519 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction pointless data scaling PHASER phasing