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Crystal structure of Alkylhydroperoxidase AhpD core (YP_425393.1) from Rhodospirillum rubrum ATCC 11170 at 1.95 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 277 NANODROP, 0.2M (NH4)2SO4, 25.0% PEG 4000, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 4.60
Crystal Properties Matthews coefficient Solvent content 2.04 39.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.683 α = 90 b = 62.683 β = 90 c = 216.707 γ = 120
Symmetry Space Group P 63 2 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 MARMOSAIC 325 mm CCD FLAT MIRROR (VERTICAL FOCUSING) 2006-12-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97925 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 1.95 48.507 98.8 0.084 14.05 5.65 19429 32.46
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 1.95 2.06 96.6 0.572 2.9 5.69
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 1.95 48.507 19375 986 100 0.197 0.195 0.2011 0.232 0.2361 RANDOM 38
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] -2.08 -1.04 -2.08 3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.936 r_dihedral_angle_4_deg 15.087 r_dihedral_angle_3_deg 12.726 r_scangle_it 5.321 r_dihedral_angle_1_deg 4.692 r_scbond_it 4.228 r_mcangle_it 2.352 r_mcbond_it 1.504 r_angle_refined_deg 1.393 r_angle_other_deg 1.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.936 r_dihedral_angle_4_deg 15.087 r_dihedral_angle_3_deg 12.726 r_scangle_it 5.321 r_dihedral_angle_1_deg 4.692 r_scbond_it 4.228 r_mcangle_it 2.352 r_mcbond_it 1.504 r_angle_refined_deg 1.393 r_angle_other_deg 1.348 r_mcbond_other 0.519 r_symmetry_vdw_refined 0.364 r_metal_ion_refined 0.341 r_nbd_refined 0.246 r_symmetry_vdw_other 0.232 r_symmetry_hbond_refined 0.227 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.175 r_nbd_other 0.17 r_symmetry_metal_ion_refined 0.136 r_nbtor_other 0.087 r_chiral_restr 0.08 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1995 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 30
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHARP phasing