1TQJ

Crystal structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 angstrom resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH629822% methyl ether PEG 2000, 200 mM MgCl2, and 100 mM MES pH 6.0, microbatch, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
2.1542.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.564α = 90
b = 87.779β = 114.58
c = 97.821γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.65094.30.052156808156808
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.61.6691.90.336

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.650148947148947786193.940.172590.172590.170160.219625%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
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.852
r_scangle_it5.601
r_scbond_it3.648
r_mcangle_it2.643
r_mcbond_it1.674
r_angle_refined_deg1.633
r_angle_other_deg1.264
r_symmetry_hbond_refined0.273
r_symmetry_vdw_other0.269
r_nbd_other0.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.852
r_scangle_it5.601
r_scbond_it3.648
r_mcangle_it2.643
r_mcbond_it1.674
r_angle_refined_deg1.633
r_angle_other_deg1.264
r_symmetry_hbond_refined0.273
r_symmetry_vdw_other0.269
r_nbd_other0.246
r_nbd_refined0.241
r_symmetry_vdw_refined0.218
r_xyhbond_nbd_refined0.162
r_chiral_restr0.108
r_nbtor_other0.088
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.002
r_xyhbond_nbd_other
r_nbtor_refined
r_metal_ion_other
r_symmetry_hbond_other
r_metal_ion_refined
r_mcbond_other
r_dihedral_angle_4_deg
r_dihedral_angle_3_deg
r_dihedral_angle_2_deg
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9869
Nucleic Acid Atoms
Solvent Atoms1439
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing