2WVM

H309A mutant of Mannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB27 in complex with GDP-alpha-D-Mannose and Mg(II)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WVLPDB ENTRY 2WVL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.2 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30-35% MPD WITH 600 MM ZNCL2 AS AN ADDITIVE, 1-5 MM GDP-ALPHA-D-MANNOSE
Crystal Properties
Matthews coefficientSolvent content
3.665.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.766α = 90
b = 112.766β = 90
c = 199.69γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
12.97748.9940.0415.42.725598
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)
12.9773.1680.60.372.092.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2WVL2.97798.1924263129294.150.176430.173550.23163RANDOM55.868
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]
3.233.23-6.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.324
r_dihedral_angle_4_deg20.468
r_dihedral_angle_3_deg19.749
r_dihedral_angle_1_deg6.6
r_scangle_it4.622
r_scbond_it2.685
r_angle_refined_deg1.642
r_mcangle_it1.34
r_mcbond_it0.656
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.324
r_dihedral_angle_4_deg20.468
r_dihedral_angle_3_deg19.749
r_dihedral_angle_1_deg6.6
r_scangle_it4.622
r_scbond_it2.685
r_angle_refined_deg1.642
r_mcangle_it1.34
r_mcbond_it0.656
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5880
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing