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Dehaloperoxidase B in complex with substrate 4-methyl-cresol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 MPEG 2000, ammonium sulphate, sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.19 43.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.206 α = 90 b = 67.402 β = 90 c = 67.803 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 RAYONIX MX300-HS 2019-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.35 37.22 99.45 0.046 0.021 0.999 35.3 4.5 56853 2 12.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.385 96.94 0.438 0.243 0.82 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3IXF 1.35 37.22 56853 3064 99.45 0.1275 0.12567 0.126 0.16096 0.1607 RANDOM 14.848
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] -0.13 -1.85 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.774 r_dihedral_angle_4_deg 20.044 r_dihedral_angle_3_deg 14.609 r_dihedral_angle_1_deg 5.255 r_rigid_bond_restr 4.085 r_long_range_B_refined 3.241 r_long_range_B_other 2.926 r_scangle_other 2.293 r_scbond_other 1.977 r_scbond_it 1.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.774 r_dihedral_angle_4_deg 20.044 r_dihedral_angle_3_deg 14.609 r_dihedral_angle_1_deg 5.255 r_rigid_bond_restr 4.085 r_long_range_B_refined 3.241 r_long_range_B_other 2.926 r_scangle_other 2.293 r_scbond_other 1.977 r_scbond_it 1.976 r_mcangle_it 1.924 r_mcangle_other 1.924 r_angle_refined_deg 1.706 r_angle_other_deg 1.586 r_mcbond_it 1.508 r_mcbond_other 1.508 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.008 r_bond_other_d 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2157 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing