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Crystal structure of HDOD domain protein with unknown function (NP_953345.1) from GEOBACTER SULFURREDUCENS at 1.90 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.2000M KThioCyanate, 20.0000% PEG-3350, No Buffer pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.567 α = 90 b = 66.631 β = 111.96 c = 54.412 γ = 90
Symmetry Space Group P 1 21 1
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 collimating mirror, toroid focusing mirror 2009-03-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97932,0.97911 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 28.375 100 0.09 0.09 11.6 3.8 24939 23.082
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 100 0.761 0.761 1.9 3.8 1820
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 1.9 28.375 24920 1268 99.96 0.182 0.18 0.185 0.226 0.2336 RANDOM 26.721
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] -1.49 0.71 1.04 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.629 r_dihedral_angle_4_deg 15.443 r_dihedral_angle_3_deg 14.375 r_scangle_it 7.655 r_scbond_it 5.441 r_dihedral_angle_1_deg 5.217 r_mcangle_it 3.179 r_mcbond_it 2.054 r_angle_refined_deg 1.574 r_angle_other_deg 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.629 r_dihedral_angle_4_deg 15.443 r_dihedral_angle_3_deg 14.375 r_scangle_it 7.655 r_scbond_it 5.441 r_dihedral_angle_1_deg 5.217 r_mcangle_it 3.179 r_mcbond_it 2.054 r_angle_refined_deg 1.574 r_angle_other_deg 1.06 r_mcbond_other 0.595 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2312 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction autoSHARP phasing