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Crystal structure of protein with unknown function from DUF364 family (ZP_00559375.1) from Desulfitobacterium hafniense DCB-2 at 2.01 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 1.0M LiCl, 0.1M citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.59 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.64 α = 90 b = 120.64 β = 90 c = 75.2 γ = 120
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 2006-04-29 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.01 28.977 99.7 0.059 0.066 12.26 7.48 41624 -3 35.519
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.08 98.1 0.668 0.815 1.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.01 28.977 41583 2092 99.95 0.173 0.171 0.215 0.2751 RANDOM 52.382
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] 0.35 0.18 0.35 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.528 r_dihedral_angle_4_deg 17.167 r_dihedral_angle_3_deg 13.183 r_dihedral_angle_1_deg 7.365 r_scangle_it 6.505 r_scbond_it 4.774 r_mcangle_it 3.037 r_mcbond_it 2.007 r_angle_refined_deg 1.428 r_angle_other_deg 0.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.528 r_dihedral_angle_4_deg 17.167 r_dihedral_angle_3_deg 13.183 r_dihedral_angle_1_deg 7.365 r_scangle_it 6.505 r_scbond_it 4.774 r_mcangle_it 3.037 r_mcbond_it 2.007 r_angle_refined_deg 1.428 r_angle_other_deg 0.846 r_mcbond_other 0.489 r_symmetry_vdw_other 0.282 r_nbd_other 0.225 r_nbd_refined 0.201 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.164 r_symmetry_hbond_refined 0.153 r_symmetry_vdw_refined 0.121 r_chiral_restr 0.089 r_nbtor_other 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3695 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction