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Crystal structure of cyanobacterial aldehyde-deformylating oxygenase 122F mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 291 0.02 M adenosine-5'-triphosphate disodium salt hydrate, 0.2M L-proline, 0.1M Hepes pH 7.1, 25%(w/v) PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.44 49.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.633 α = 90 b = 61.838 β = 90 c = 125.315 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 ADSC QUANTUM 315 2014-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.98 SSRF BL17U
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 2.9 50 84.9 11194 9504
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 2.9 2.95 99.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4QUW 2.9 41.224 10660 8494 432 79.68 0.2714 0.27014 0.2653 0.29685 0.2893 RANDOM 43.904
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] -1.97 0.46 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.597 r_dihedral_angle_3_deg 19.999 r_dihedral_angle_4_deg 16.58 r_long_range_B_refined 6.575 r_long_range_B_other 6.561 r_dihedral_angle_1_deg 5.53 r_scangle_other 3.857 r_angle_other_deg 3.547 r_mcangle_it 2.931 r_mcangle_other 2.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.597 r_dihedral_angle_3_deg 19.999 r_dihedral_angle_4_deg 16.58 r_long_range_B_refined 6.575 r_long_range_B_other 6.561 r_dihedral_angle_1_deg 5.53 r_scangle_other 3.857 r_angle_other_deg 3.547 r_mcangle_it 2.931 r_mcangle_other 2.931 r_scbond_it 2.639 r_scbond_other 2.639 r_mcbond_other 1.733 r_mcbond_it 1.732 r_angle_refined_deg 1.634 r_chiral_restr 0.073 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 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 3430 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 4
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling