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Crystal structure of ribulose-5-phosphate 3-epimerase (YP_718263.1) from Haemophilus somnus 129PT at 1.91 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.17 277 NANODROP, 16.0% PEG 8000, 0.167M Calcium acetate, 0.1M MES pH 6.17, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.71 54.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.01 α = 90 b = 85.01 β = 90 c = 140.16 γ = 120
Symmetry Space Group P 31 2 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 mirror (vertical focusing) 2008-02-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97922, 0.97840 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 1.91 28.916 99.8 0.12 7.72 46203 -3 19.326
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 1.91 1.98 99.8 0.764 1.4
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 1.91 28.916 46156 2335 99.83 0.168 0.166 0.1713 0.205 0.2077 RANDOM 17.224
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] 0.46 0.23 0.46 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.868 r_dihedral_angle_3_deg 11.59 r_dihedral_angle_4_deg 10.886 r_scangle_it 7.008 r_dihedral_angle_1_deg 5.515 r_scbond_it 4.969 r_mcangle_it 3.288 r_mcbond_it 2.032 r_angle_refined_deg 1.611 r_angle_other_deg 1.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.868 r_dihedral_angle_3_deg 11.59 r_dihedral_angle_4_deg 10.886 r_scangle_it 7.008 r_dihedral_angle_1_deg 5.515 r_scbond_it 4.969 r_mcangle_it 3.288 r_mcbond_it 2.032 r_angle_refined_deg 1.611 r_angle_other_deg 1.101 r_mcbond_other 0.583 r_chiral_restr 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3693 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing