2VF5

Glucosamine-6-phosphate synthase in complex with glucosamine-6- phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MOQPDB ENTRY 1MOQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.58% PEG4000, 0.2 M SODIUM ACETATE PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.5852.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.762α = 90
b = 144.762β = 90
c = 171.447γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.92099.20.085.34.615522
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)
12.93.0699.20.511.54.7

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 1MOQ2.9151458176799.90.2180.2170.242RANDOM27.46
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]
0.10.050.1-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.06
r_scangle_it3.249
r_angle_refined_deg2.115
r_scbond_it2.002
r_mcangle_it1.136
r_mcbond_it0.612
r_nbd_refined0.28
r_symmetry_vdw_refined0.256
r_symmetry_hbond_refined0.228
r_xyhbond_nbd_refined0.181
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.06
r_scangle_it3.249
r_angle_refined_deg2.115
r_scbond_it2.002
r_mcangle_it1.136
r_mcbond_it0.612
r_nbd_refined0.28
r_symmetry_vdw_refined0.256
r_symmetry_hbond_refined0.228
r_xyhbond_nbd_refined0.181
r_chiral_restr0.146
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
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_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 Atoms2820
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing