2H4L

Complex of PMM/PGM with ribose 1-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P5D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293NA, K TARTRATE , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1943.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.717α = 90
b = 74.095β = 90
c = 84.347γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C1.0398APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.45091.74.216595
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4983.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1P5D2.443.851560080391.660.189980.189980.186460.25946same as 1P5d22.416
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]
-0.98-2.283.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.323
r_dihedral_angle_3_deg14.698
r_dihedral_angle_4_deg14.54
r_dihedral_angle_1_deg5.536
r_scangle_it1.707
r_angle_refined_deg1.192
r_scbond_it1.056
r_mcangle_it0.701
r_mcbond_it0.403
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.323
r_dihedral_angle_3_deg14.698
r_dihedral_angle_4_deg14.54
r_dihedral_angle_1_deg5.536
r_scangle_it1.707
r_angle_refined_deg1.192
r_scbond_it1.056
r_mcangle_it0.701
r_mcbond_it0.403
r_nbtor_refined0.3
r_nbd_refined0.191
r_metal_ion_refined0.183
r_symmetry_vdw_refined0.183
r_symmetry_hbond_refined0.181
r_xyhbond_nbd_refined0.147
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3430
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data scaling