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Crystal structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 angstrom resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6 298 22% methyl ether PEG 2000, 200 mM MgCl2, and 100 mM MES pH 6.0, microbatch, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.564 α = 90 b = 87.779 β = 114.58 c = 97.821 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 ADSC QUANTUM 4 2002-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
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 1.6 50 94.3 0.052 156808 156808
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) 1.6 1.66 91.9 0.336
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT 1.6 50 148947 148947 7861 93.94 0.17259 0.17259 0.17016 0.183 0.21962 0.2257 5% 21.576
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] 0.3 -0.6 -0.39 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.852 r_scangle_it 5.601 r_scbond_it 3.648 r_mcangle_it 2.643 r_mcbond_it 1.674 r_angle_refined_deg 1.633 r_angle_other_deg 1.264 r_symmetry_hbond_refined 0.273 r_symmetry_vdw_other 0.269 r_nbd_other 0.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.852 r_scangle_it 5.601 r_scbond_it 3.648 r_mcangle_it 2.643 r_mcbond_it 1.674 r_angle_refined_deg 1.633 r_angle_other_deg 1.264 r_symmetry_hbond_refined 0.273 r_symmetry_vdw_other 0.269 r_nbd_other 0.246 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.218 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.108 r_nbtor_other 0.088 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9869 Nucleic Acid Atoms Solvent Atoms 1439 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling COMO phasing