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Structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PJ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 15% PEG 2000MME, 0.2M MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.62 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.621 α = 90 b = 223.74 β = 90 c = 119.371 γ = 90
Symmetry Space Group C 2 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 IMAGE PLATE MARRESEARCH 2002-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.9 EMBL/DESY, HAMBURG X11
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 2.1 20 88.3 0.073 6.2 2.5 46564 46564
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.15 84.5
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 FOURIER SYNTHESIS THROUGHOUT 1PJ6 2.1 20 46564 46564 2482 100 0.16253 0.16253 0.15934 0.1597 0.22172 0.2199 RANDOM 33.336
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] -1.02 -0.57 1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.771 r_dihedral_angle_1_deg 6.522 r_scangle_it 4.96 r_scbond_it 3.238 r_angle_refined_deg 1.831 r_mcangle_it 1.786 r_mcbond_it 1.037 r_symmetry_hbond_refined 0.353 r_symmetry_vdw_refined 0.263 r_nbd_refined 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.771 r_dihedral_angle_1_deg 6.522 r_scangle_it 4.96 r_scbond_it 3.238 r_angle_refined_deg 1.831 r_mcangle_it 1.786 r_mcbond_it 1.037 r_symmetry_hbond_refined 0.353 r_symmetry_vdw_refined 0.263 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6237 Nucleic Acid Atoms Solvent Atoms 778 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing