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Crystal structure of a putative membrane protein of unknown function (yfdx) from klebsiella pneumoniae subsp. at 1.65 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 277 20.0000% PEG-3350, 0.2000M ZnAcetate, No Buffer pH 6.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.29 46.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.207 α = 90 b = 79.016 β = 90 c = 137.99 γ = 90
Symmetry Space Group P 21 21 21
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) 2008-06-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97937,0.91837,0.97874 SSRL BL11-1
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 1.65 29.975 99.9 0.11 0.11 6.1 3.9 90273 13.584
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) 1.65 1.69 99.8 0.618 0.618 1.2 3.9 6587
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 MAD THROUGHOUT 1.65 29.975 90207 4525 99.84 0.154 0.152 0.194 0.1863 RANDOM 10.232
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] 1.03 -0.59 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.478 r_dihedral_angle_4_deg 21.599 r_dihedral_angle_3_deg 13.116 r_scangle_it 6.363 r_scbond_it 4.889 r_dihedral_angle_1_deg 4.681 r_mcangle_it 2.39 r_mcbond_it 1.99 r_angle_refined_deg 1.387 r_angle_other_deg 0.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.478 r_dihedral_angle_4_deg 21.599 r_dihedral_angle_3_deg 13.116 r_scangle_it 6.363 r_scbond_it 4.889 r_dihedral_angle_1_deg 4.681 r_mcangle_it 2.39 r_mcbond_it 1.99 r_angle_refined_deg 1.387 r_angle_other_deg 0.909 r_mcbond_other 0.69 r_symmetry_vdw_other 0.274 r_symmetry_vdw_refined 0.251 r_symmetry_hbond_refined 0.232 r_nbd_refined 0.218 r_metal_ion_refined 0.188 r_nbd_other 0.183 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.173 r_nbtor_other 0.088 r_chiral_restr 0.085 r_bond_refined_d 0.015 r_symmetry_metal_ion_refined 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5314 Nucleic Acid Atoms Solvent Atoms 1090 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing