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Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 15% PEG 2000MME, 0.2 MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.61 52.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.877 α = 90 b = 222.506 β = 90 c = 119.304 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 2002-05-01 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 1.65 15 99.3 0.067 11.9 5.4 106504 106504
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.7 99
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 1PJ5 1.65 14.84 106504 106504 5618 100 0.15752 0.15752 0.15567 0.1564 0.19283 0.1929 RANDOM 25.253
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 12.159 r_dihedral_angle_1_deg 5.951 r_scangle_it 4.049 r_scbond_it 2.53 r_angle_refined_deg 1.634 r_mcangle_it 1.582 r_mcbond_it 0.923 r_symmetry_vdw_refined 0.294 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 12.159 r_dihedral_angle_1_deg 5.951 r_scangle_it 4.049 r_scbond_it 2.53 r_angle_refined_deg 1.634 r_mcangle_it 1.582 r_mcbond_it 0.923 r_symmetry_vdw_refined 0.294 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.203 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6285 Nucleic Acid Atoms Solvent Atoms 1612 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing