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Dithionite reduced L-alpha-Glycerophosphate Oxidase from Mycoplasma pneumoniae with FAD bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X9M PDB ENTRY 4X9M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277.15 2.68 M NaCl, 2% v/v isopropanol, and 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.66 53.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.605 α = 90 b = 111.605 β = 90 c = 111.605 γ = 90
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 315r 2010-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.9765 ALS 5.0.3
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 2.499 55.8 100 19.9 51.1 16368
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 2.499 2.64 100 3 28.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4X9M 2.499 55.8 15520 831 99.98 0.14952 0.14634 0.1539 0.20997 0.208 RANDOM 43.993
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.775 r_dihedral_angle_4_deg 20.86 r_dihedral_angle_3_deg 15.444 r_dihedral_angle_1_deg 6.683 r_long_range_B_refined 6.55 r_long_range_B_other 6.489 r_scangle_other 5.051 r_mcangle_it 3.739 r_mcangle_other 3.738 r_scbond_it 3.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.775 r_dihedral_angle_4_deg 20.86 r_dihedral_angle_3_deg 15.444 r_dihedral_angle_1_deg 6.683 r_long_range_B_refined 6.55 r_long_range_B_other 6.489 r_scangle_other 5.051 r_mcangle_it 3.739 r_mcangle_other 3.738 r_scbond_it 3.339 r_scbond_other 3.339 r_mcbond_it 2.6 r_mcbond_other 2.599 r_angle_refined_deg 1.622 r_angle_other_deg 0.965 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3000 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling Coot model building