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Crystal structure of the Methanocaldococcus jannaschii G1PDH with NADPH and DHAP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RFL PDB ENTRY 4RFL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 294 30% (v/v) P550MME/P20K, 0.1 M hepes, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.47 50.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.382 α = 77.52 b = 71.898 β = 79.54 c = 101.697 γ = 75.6
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 210r 2013-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.91160 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.22 46.66 98.2 77389 76018 1 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.22 2.35 96.5 0.778 1.8 3.9 10895
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 (All) 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 4RFL 2.23 46.66 77389 71776 3887 97.66 0.1822 0.18452 0.1822 0.1891 0.22865 0.234 RANDOM 36.368
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] -1.71 1.03 0.16 2.99 1.97 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.269 r_dihedral_angle_4_deg 18.192 r_dihedral_angle_3_deg 17.961 r_long_range_B_refined 6.826 r_long_range_B_other 6.823 r_dihedral_angle_1_deg 5.336 r_scangle_other 4.869 r_mcangle_it 3.918 r_mcangle_other 3.918 r_scbond_it 3.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.269 r_dihedral_angle_4_deg 18.192 r_dihedral_angle_3_deg 17.961 r_long_range_B_refined 6.826 r_long_range_B_other 6.823 r_dihedral_angle_1_deg 5.336 r_scangle_other 4.869 r_mcangle_it 3.918 r_mcangle_other 3.918 r_scbond_it 3.233 r_scbond_other 3.233 r_angle_other_deg 2.761 r_mcbond_it 2.623 r_mcbond_other 2.623 r_angle_refined_deg 1.591 r_chiral_restr 0.091 r_gen_planes_other 0.023 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10366 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms 316
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling