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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, 34% PEG 4000, PH 5.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Crystal Properties Matthews coefficient Solvent content 2.11 41.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.678 α = 90 b = 66.505 β = 90 c = 68.25 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 2007-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.000 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 98 0.052 25.36 3.5 66582 2 14.63
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 1.26 1.29 93.5 0.536 2 3.3 4897
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 70107 66582 3525 98 0.178 0.176 0.1734 0.201 0.1989 RANDOM 14.63
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] -0.51 0.13 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.077 r_dihedral_angle_4_deg 20.53 r_dihedral_angle_3_deg 14.751 r_dihedral_angle_1_deg 4.061 r_scangle_it 2.693 r_scbond_it 1.935 r_mcangle_it 1.399 r_angle_refined_deg 1.107 r_mcbond_it 0.893 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.077 r_dihedral_angle_4_deg 20.53 r_dihedral_angle_3_deg 14.751 r_dihedral_angle_1_deg 4.061 r_scangle_it 2.693 r_scbond_it 1.935 r_mcangle_it 1.399 r_angle_refined_deg 1.107 r_mcbond_it 0.893 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.092 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2182 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 110
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling