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Crystal structure of a D-ribulose-5-phosphate-3-epimerase (NP_954699) from HOMO SAPIENS at 2.20 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 0.16M magnesium acetate, 10.0% polyethylene glycol 8000, 20.0% Glycerol, 0.1M sodium cacodylate pH 6.0, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.48 50.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.665 α = 90 b = 47.665 β = 90 c = 220.774 γ = 90
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) 2009-12-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97944,0.97894 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 2.2 29.127 97.6 0.095 8.35 24823 -3 30.791
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 2.2 2.28 96.4 0.651 1.6
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 2.2 29.127 24753 1263 99.57 0.1667 0.1644 0.169 0.2112 0.2092 RANDOM 46.987
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] 1.76 1.76 -3.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.536 r_dihedral_angle_4_deg 18.958 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_1_deg 4.298 r_scangle_it 2.849 r_scbond_it 2.018 r_angle_refined_deg 1.614 r_mcangle_it 1.108 r_angle_other_deg 1.029 r_mcbond_it 0.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.536 r_dihedral_angle_4_deg 18.958 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_1_deg 4.298 r_scangle_it 2.849 r_scbond_it 2.018 r_angle_refined_deg 1.614 r_mcangle_it 1.108 r_angle_other_deg 1.029 r_mcbond_it 0.609 r_mcbond_other 0.176 r_chiral_restr 0.094 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3399 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 18
Software Software Software Name Purpose SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing