5J9G

Structure of Lactobacillus acidophilus glyceraldehyde-3-phosphate dehydrogenase at 2.21 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4QX6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.429510% w/v PEG 1000, 10% w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.4148.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.99α = 90
b = 114.99β = 90
c = 113.3γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++VARIMAX HF2015-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.2138.3399.90.0930.99916.517.23843740.2

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 REPLACEMENTTHROUGHOUT4QX62.2138.3335675170897.290.204270.203250.2262RANDOM44.76
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]
-0.59-0.591.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.279
r_dihedral_angle_4_deg16.08
r_dihedral_angle_3_deg12.569
r_dihedral_angle_1_deg6.756
r_long_range_B_refined2.824
r_long_range_B_other2.798
r_angle_refined_deg1.525
r_mcangle_it1.487
r_mcangle_other1.487
r_scangle_other1.449
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.279
r_dihedral_angle_4_deg16.08
r_dihedral_angle_3_deg12.569
r_dihedral_angle_1_deg6.756
r_long_range_B_refined2.824
r_long_range_B_other2.798
r_angle_refined_deg1.525
r_mcangle_it1.487
r_mcangle_other1.487
r_scangle_other1.449
r_angle_other_deg1.2
r_scbond_it0.877
r_scbond_other0.877
r_mcbond_other0.865
r_mcbond_it0.864
r_chiral_restr0.101
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.003
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 Atoms5126
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing