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Crystal structure of a putative dyp-type peroxidase protein (so_0740) from shewanella oneidensis at 2.75 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 7.5 277 5.0% iso-Propanol, 20.0% PEG-4000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.61 65.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.31 α = 90 b = 94.31 β = 90 c = 113.68 γ = 90
Symmetry Space Group P 43 21 2
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 ADSC QUANTUM 315 Flat mirror (vertical focusing) 2006-04-24 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979291, 0.918370, 0.978940 SSRL BL11-1
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 2.75 29.54 95.4 0.107 10.85 13932 58.902
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 2.75 2.85 86.7 0.835 1.7 2297
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.75 29.54 13888 691 99.72 0.193 0.191 0.1979 0.229 0.2437 RANDOM 58.485
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] -2 -2 3.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.04 r_dihedral_angle_3_deg 15.824 r_dihedral_angle_4_deg 12.404 r_dihedral_angle_1_deg 6.927 r_mcangle_it 3.803 r_scangle_it 3.761 r_mcbond_it 2.67 r_scbond_it 2.574 r_angle_refined_deg 1.134 r_angle_other_deg 0.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.04 r_dihedral_angle_3_deg 15.824 r_dihedral_angle_4_deg 12.404 r_dihedral_angle_1_deg 6.927 r_mcangle_it 3.803 r_scangle_it 3.761 r_mcbond_it 2.67 r_scbond_it 2.574 r_angle_refined_deg 1.134 r_angle_other_deg 0.615 r_mcbond_other 0.532 r_nbd_refined 0.228 r_symmetry_vdw_other 0.215 r_nbd_other 0.212 r_symmetry_hbond_refined 0.203 r_nbtor_refined 0.198 r_xyhbond_nbd_refined 0.146 r_symmetry_vdw_refined 0.146 r_nbtor_other 0.093 r_chiral_restr 0.063 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2453 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms
Software Software Software Name Purpose MolProbity model building REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SOLVE phasing RESOLVE phasing