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Crystal structure of the apo form of cyanobacterial aldehyde-deformylating oxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OC5 PDB ENTRY 2OC5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.2M Magnesium chloride hexahydrate, 0.1M Tris hydrochloride pH 8.5, 30% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.99 38.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.682 α = 90 b = 61.682 β = 90 c = 110.461 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2012-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5418
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 2.26 50 99.7 10566 10534
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 2.26 2.3 99.8
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 PDB ENTRY 2OC5 2.26 41.15 10054 10003 505 99.49 0.22857 0.22668 0.2245 0.26576 0.2613 RANDOM 34.962
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] 0.93 0.93 -1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.08 r_dihedral_angle_3_deg 16.579 r_dihedral_angle_4_deg 13.193 r_long_range_B_refined 5.944 r_long_range_B_other 5.939 r_scangle_other 4.933 r_dihedral_angle_1_deg 4.781 r_scbond_other 3.66 r_angle_other_deg 3.572 r_scbond_it 3.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.08 r_dihedral_angle_3_deg 16.579 r_dihedral_angle_4_deg 13.193 r_long_range_B_refined 5.944 r_long_range_B_other 5.939 r_scangle_other 4.933 r_dihedral_angle_1_deg 4.781 r_scbond_other 3.66 r_angle_other_deg 3.572 r_scbond_it 3.454 r_mcangle_other 3.287 r_mcangle_it 3.284 r_mcbond_it 2.304 r_mcbond_other 2.298 r_angle_refined_deg 1.294 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_other 0.01 r_gen_planes_refined 0.005 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 1789 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 17
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling