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OxyA from Actinoplanes teichomyceticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M Mes/ NaOH pH 6.5, 14.4% (w/ v) PEG 8,000, 20% (v/ v) glycerol, 0.16 M calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.59 52.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.49 α = 90 b = 103.06 β = 90 c = 152.97 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2012-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.07169 SLS X10SA
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 48.85 100 0.083 20 13.1 54785 46
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 2.1 2.2 99.9 0.744 4.3
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 5EX8 2.1 48.83 52043 2742 99.96 0.19969 0.19817 0.2047 0.22859 0.2353 RANDOM 54.104
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] -1.8 1.99 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.561 r_dihedral_angle_4_deg 16.884 r_dihedral_angle_3_deg 13.871 r_dihedral_angle_1_deg 5.643 r_long_range_B_refined 5.066 r_long_range_B_other 5.066 r_scangle_other 1.97 r_mcangle_it 1.671 r_mcangle_other 1.671 r_angle_refined_deg 1.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.561 r_dihedral_angle_4_deg 16.884 r_dihedral_angle_3_deg 13.871 r_dihedral_angle_1_deg 5.643 r_long_range_B_refined 5.066 r_long_range_B_other 5.066 r_scangle_other 1.97 r_mcangle_it 1.671 r_mcangle_other 1.671 r_angle_refined_deg 1.349 r_scbond_it 1.215 r_scbond_other 1.215 r_mcbond_it 1.01 r_mcbond_other 1.007 r_angle_other_deg 0.956 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 6084 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing