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Crystal structure of alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein (YP_296737.1) from Ralstonia eutropha JMP134 at 2.15 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.1 277 NANODROP, 0.2M Na2HPO4, 20.0% PEG 3350, No Buffer pH 9.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.65 53.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.105 α = 84.26 b = 93.953 β = 81.64 c = 120.898 γ = 77.73
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 325 mm CCD Flat mirror (vertical focusing) 2006-12-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97932, 0.97905 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 1.88 48.912 87.2 0.079 6.23 211872 30.222
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 1.88 1.95 77.4 0.419 2 18037
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 (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 MAD THROUGHOUT 2.15 48.912 152688 7726 94.68 0.213 0.213 0.211 0.2201 0.262 0.2687 RANDOM 32.806
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] 0.94 -2.42 -2.97 -0.85 4.05 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.13 r_dihedral_angle_4_deg 11.107 r_dihedral_angle_3_deg 10.693 r_scangle_it 6.123 r_scbond_it 4.919 r_dihedral_angle_1_deg 3.232 r_mcangle_it 2.393 r_angle_refined_deg 1.535 r_mcbond_it 1.523 r_angle_other_deg 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.13 r_dihedral_angle_4_deg 11.107 r_dihedral_angle_3_deg 10.693 r_scangle_it 6.123 r_scbond_it 4.919 r_dihedral_angle_1_deg 3.232 r_mcangle_it 2.393 r_angle_refined_deg 1.535 r_mcbond_it 1.523 r_angle_other_deg 0.96 r_mcbond_other 0.681 r_xyhbond_nbd_refined 0.231 r_symmetry_hbond_refined 0.224 r_nbd_refined 0.213 r_symmetry_vdw_other 0.196 r_nbtor_refined 0.184 r_nbd_other 0.162 r_symmetry_vdw_refined 0.109 r_chiral_restr 0.093 r_nbtor_other 0.089 r_xyhbond_nbd_other 0.052 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17690 Nucleic Acid Atoms Solvent Atoms 1338 Heterogen Atoms 245
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing