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Crystal structure of apocarotenoid cleavage oxygenase from Synechocystis, native enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other ACO APO FORM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.7 pH 5.70
Crystal Properties Matthews coefficient Solvent content 3.6 66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.046 α = 90 b = 125.278 β = 90 c = 203.086 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 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.39 44 93.3 0.06 10.8 2.7 111472 55.8
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 2.39 2.5 80.9 0.46 2.1
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 ACO APO FORM 2.39 44.41 111472 5864 97.9 0.182 0.18 0.1868 0.224 0.2292 RANDOM 64.26
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] 1.11 -0.84 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.548 r_dihedral_angle_4_deg 16.76 r_dihedral_angle_3_deg 16.092 r_dihedral_angle_1_deg 6.997 r_scangle_it 2.754 r_scbond_it 1.758 r_angle_refined_deg 1.609 r_mcangle_it 1.113 r_mcbond_it 0.671 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.548 r_dihedral_angle_4_deg 16.76 r_dihedral_angle_3_deg 16.092 r_dihedral_angle_1_deg 6.997 r_scangle_it 2.754 r_scbond_it 1.758 r_angle_refined_deg 1.609 r_mcangle_it 1.113 r_mcbond_it 0.671 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.214 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15068 Nucleic Acid Atoms Solvent Atoms 542 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing