4LRD

Phosphopentomutase 4H11 variant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M8ZPDB ENTRY 3M8Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.4529320 mg/mL protein in 1 mM manganese chloride, 25 mM Tris-HCl, pH 7.4 against a reservoir of 25% PEG3350, 50 mM ammonium sulfate, 100 mM Bis-Tris, pH 5.45, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9938.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.293α = 90
b = 60.492β = 98.5
c = 78.854γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.979APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.785099.50.07315.334906-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.8199.70.2533.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3M8Z1.7839.023348733246164499.280.141690.139760.17964RANDOM14.063
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]
0.090.270.08-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.867
r_dihedral_angle_4_deg14.753
r_dihedral_angle_3_deg13.137
r_dihedral_angle_1_deg6.301
r_long_range_B_refined5.97
r_long_range_B_other5.969
r_scangle_other3.747
r_scbond_it2.445
r_scbond_other2.445
r_angle_refined_deg2.028
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.867
r_dihedral_angle_4_deg14.753
r_dihedral_angle_3_deg13.137
r_dihedral_angle_1_deg6.301
r_long_range_B_refined5.97
r_long_range_B_other5.969
r_scangle_other3.747
r_scbond_it2.445
r_scbond_other2.445
r_angle_refined_deg2.028
r_mcangle_it1.731
r_mcangle_other1.73
r_mcbond_it1.142
r_mcbond_other1.133
r_angle_other_deg0.941
r_chiral_restr0.133
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3071
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing