6H90

K145A variant of beta-phosphoglucomutase from Lactococcus lactis inhibited by beryllium trifluoride to 1.3 A.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WHE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.229124-34% PEG 4000 200mM sodium acetate 100mM TRIS pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.3647.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.32α = 90
b = 53.63β = 90
c = 81.5γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.3140.7599.90.0680.0810.0320.99913.16.555835
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.311.3499.91.1011.3350.5170.5391.56.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2WHE1.3140.7552935283299.890.136720.135250.1627RANDOM16.262
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]
0.61-0.38-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.914
r_sphericity_free21.785
r_dihedral_angle_4_deg20.832
r_dihedral_angle_3_deg12.318
r_sphericity_bonded10.66
r_dihedral_angle_1_deg5.318
r_long_range_B_other3.191
r_long_range_B_refined3.188
r_scangle_other2.894
r_scbond_it2.426
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.914
r_sphericity_free21.785
r_dihedral_angle_4_deg20.832
r_dihedral_angle_3_deg12.318
r_sphericity_bonded10.66
r_dihedral_angle_1_deg5.318
r_long_range_B_other3.191
r_long_range_B_refined3.188
r_scangle_other2.894
r_scbond_it2.426
r_scbond_other2.426
r_rigid_bond_restr1.915
r_mcangle_it1.716
r_mcangle_other1.715
r_angle_refined_deg1.49
r_mcbond_it1.332
r_mcbond_other1.332
r_angle_other_deg1.08
r_chiral_restr0.217
r_bond_refined_d0.012
r_gen_planes_refined0.009
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1685
Nucleic Acid Atoms
Solvent Atoms289
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
xia2data reduction
MOLREPphasing