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Crystal structure of the Methanocaldococcus jannaschii G1PDH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CE9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 30% (v/v) P550MME/P20K, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.16 43.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.765 α = 90 b = 59.552 β = 90.39 c = 119.825 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 315 2012-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.91840 Australian Synchrotron MX2
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 2.45 46.07 98.4 25465 25920 1 2
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 2.45 2.56 98.5 0.551 2 3.1 3089
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 3CE9 2.45 46.07 25465 24057 1318 0.19488 0.1928 0.19282 0.1973 0.23074 0.2338 RANDOM 61.576
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] 1.82 -0.04 1.03 -2.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.677 r_dihedral_angle_3_deg 21.074 r_dihedral_angle_4_deg 20.736 r_long_range_B_refined 5.413 r_long_range_B_other 5.413 r_dihedral_angle_1_deg 5.351 r_scangle_other 3.924 r_mcangle_it 3.343 r_mcangle_other 3.342 r_scbond_it 2.641
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.677 r_dihedral_angle_3_deg 21.074 r_dihedral_angle_4_deg 20.736 r_long_range_B_refined 5.413 r_long_range_B_other 5.413 r_dihedral_angle_1_deg 5.351 r_scangle_other 3.924 r_mcangle_it 3.343 r_mcangle_other 3.342 r_scbond_it 2.641 r_scbond_other 2.641 r_angle_other_deg 2.503 r_mcbond_it 2.19 r_mcbond_other 2.19 r_angle_refined_deg 1.526 r_chiral_restr 0.092 r_gen_planes_other 0.016 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5164 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 4
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling