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X-ray Crystal Structure Analysis of the Binding Site in the Ferric and Oxyferrous Forms of the Recombinant Heme Dehaloperoxidase Cloned from Amphitrite ornata
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 277 26-32% PEG 4000,0.2M ammonium sulfate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.21 44.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.686 α = 90 b = 67.572 β = 90 c = 67.622 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 IMAGE PLATE RIGAKU RAXIS IV++ Osmic optics 2006-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 1.62 25.62 99.8 0.044 23.7 5.7 36016 2 2
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) 1.62 1.68 98.8 0.295 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.62 25.62 36001 34161 1795 99.88 0.19389 0.19146 0.1896 0.23947 0.2368 RANDOM 17.646
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] 0.11 -0.04 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.69 r_dihedral_angle_4_deg 24.887 r_dihedral_angle_3_deg 15.433 r_sphericity_free 5.051 r_dihedral_angle_1_deg 4.371 r_scangle_it 3.553 r_scbond_it 3.132 r_rigid_bond_restr 3.023 r_sphericity_bonded 2.936 r_mcangle_it 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.69 r_dihedral_angle_4_deg 24.887 r_dihedral_angle_3_deg 15.433 r_sphericity_free 5.051 r_dihedral_angle_1_deg 4.371 r_scangle_it 3.553 r_scbond_it 3.132 r_rigid_bond_restr 3.023 r_sphericity_bonded 2.936 r_mcangle_it 1.55 r_angle_refined_deg 1.254 r_mcbond_it 1.019 r_nbtor_refined 0.304 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.219 r_symmetry_hbond_refined 0.131 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2397 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 104
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling