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X-ray structure of the metcyano form of dehaloperoxidase from amphitrite ornata: evidence for photoreductive lysis of iron-cyanide bond
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EW6 PDB ENTRY 1EW6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 277 0.2 M AMMONIUM SULFATE, 28% PEG 4000, PH 5.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Crystal Properties Matthews coefficient Solvent content 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.252 α = 90 b = 66.55 β = 90 c = 68.713 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 MARMOSAIC 225 mm CCD 2007-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
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 1.26 35 99.1 0.053 218.6 3.5 70910 67355 2 11.94
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 1.26 1.29 95.6 0.324 0.324 2.6 3.3 4989
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1EW6 1.26 35 2 70910 67355 3555 99.1 0.155 0.153 0.1525 0.186 0.1849 RANDOM 11.94
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] 0.12 0.02 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.165 r_dihedral_angle_4_deg 18.314 r_dihedral_angle_3_deg 14.54 r_dihedral_angle_1_deg 4.112 r_scangle_it 2.271 r_scbond_it 1.645 r_mcangle_it 1.14 r_angle_refined_deg 1.026 r_mcbond_it 0.706 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.165 r_dihedral_angle_4_deg 18.314 r_dihedral_angle_3_deg 14.54 r_dihedral_angle_1_deg 4.112 r_scangle_it 2.271 r_scbond_it 1.645 r_mcangle_it 1.14 r_angle_refined_deg 1.026 r_mcbond_it 0.706 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.203 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.122 r_chiral_restr 0.086 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2182 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 100
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling