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Oxidized 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 3DME
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, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.71 54.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.59 α = 90 b = 111.59 β = 90 c = 111.59 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 2.4 50 100 22.7 23.4 18401
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 2.4 2.53 99 4.4 23.6
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 3DME 2.4 49.9 17440 923 99.77 0.15044 0.14762 0.1556 0.20376 0.2063 RANDOM 37.397
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 39.262 r_dihedral_angle_4_deg 21.569 r_dihedral_angle_3_deg 16.234 r_long_range_B_refined 7.172 r_long_range_B_other 7.111 r_dihedral_angle_1_deg 6.853 r_scangle_other 5.494 r_scbond_it 3.673 r_scbond_other 3.673 r_mcangle_it 3.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.262 r_dihedral_angle_4_deg 21.569 r_dihedral_angle_3_deg 16.234 r_long_range_B_refined 7.172 r_long_range_B_other 7.111 r_dihedral_angle_1_deg 6.853 r_scangle_other 5.494 r_scbond_it 3.673 r_scbond_other 3.673 r_mcangle_it 3.37 r_mcangle_other 3.37 r_mcbond_it 2.437 r_mcbond_other 2.435 r_angle_refined_deg 1.802 r_angle_other_deg 0.986 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 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 64
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling Coot model building PHASER phasing