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Structure of Phenoxazinone synthase from Streptomyces antibioticus reveals a new type 2 copper center.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GSK PDB ENTRY 1GSK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 278 PEG 4000, SODIUM CITRATE, 2- PROPANOL, GLYCEROL, PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 288K, PH 5.00, temperature 278K
Crystal Properties Matthews coefficient Solvent content 3.13 60.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.494 α = 117.04 b = 163.456 β = 95.74 c = 164.352 γ = 107.23
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2003-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.3 55.4 86.3 0.082 0.058 11.6 2.4 357511 36.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.41 72.4 0.4 0.28 2.6 2.2
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 1GSK 2.3 20 339025 17920 86.34 0.16743 0.16453 0.1646 0.22237 0.2224 RANDOM 27.202
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] -0.15 -0.02 -0.03 0.03 0.15 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.007 r_dihedral_angle_4_deg 22.079 r_dihedral_angle_3_deg 15.281 r_dihedral_angle_1_deg 8.089 r_scangle_it 3.402 r_mcangle_it 3.034 r_scbond_it 2.402 r_mcbond_it 1.982 r_angle_refined_deg 1.585 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.007 r_dihedral_angle_4_deg 22.079 r_dihedral_angle_3_deg 15.281 r_dihedral_angle_1_deg 8.089 r_scangle_it 3.402 r_mcangle_it 3.034 r_scbond_it 2.402 r_mcbond_it 1.982 r_angle_refined_deg 1.585 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 54720 Nucleic Acid Atoms Solvent Atoms 4377 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement CNS refinement CrystalClear data collection MOSFLM data reduction CCP4 data scaling CNS phasing