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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 2.12 42.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.938 α = 90 b = 67.091 β = 90 c = 68.402 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 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 35 99.8 0.058 14.8 5.7 34478 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 99.5 0.553 5.4 3388
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 35 2 34585 34429 1738 99.63 0.173 0.173 0.17 0.1824 0.224 0.2234 RANDOM 17.372
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] -0.18 0.04 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.045 r_dihedral_angle_4_deg 15.295 r_dihedral_angle_3_deg 14.538 r_dihedral_angle_1_deg 4.311 r_scangle_it 3.733 r_scbond_it 2.647 r_mcangle_it 1.618 r_angle_refined_deg 1.162 r_mcbond_it 1.055 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.045 r_dihedral_angle_4_deg 15.295 r_dihedral_angle_3_deg 14.538 r_dihedral_angle_1_deg 4.311 r_scangle_it 3.733 r_scbond_it 2.647 r_mcangle_it 1.618 r_angle_refined_deg 1.162 r_mcbond_it 1.055 r_nbtor_refined 0.299 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2414 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 107
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