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Tetrameric form of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GMB PDB ENTRY 3GMB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 1.0M Lithium sulfate, 6% PEG 8000, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.21 70.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.838 α = 90 b = 103.838 β = 90 c = 452.781 γ = 120
Symmetry Space Group P 31 2 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 RAYONIX MX225HE 2012-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.98 50 98.7 0.102 11.2 10.5 195890 22.74
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 1.98 2.01 95.2 0.372 7.8 10.3 9302
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3GMB 1.981 43.905 1.33 195631 9852 98.86 0.1731 0.1717 0.1685 0.1997 0.1962 24.8726
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] 0.1803 0.1803 -0.3607
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.512 f_angle_d 1.418 f_chiral_restr 0.086 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11499 Nucleic Acid Atoms Solvent Atoms 1378 Heterogen Atoms 705
Software Software Software Name Purpose HKL-2000 data collection PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling