4MVJ

2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3-phosphate Dehydrogenase A (gapA) from Escherichia coli Modified by Acetyl Phosphate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S7C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295Protein - 7.3mg/mL, 0.15M Sodium chloride, 0.01M Tris-HCl pH 8.3, Screen - PACT (G2), 0.2 M Sodium bromide, 0.1 M Bis Tris propane pH 7.5, 20 % (w/v) PEG 3350, 10mM ACP., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2244.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.879α = 90
b = 69.688β = 98.8
c = 271.923γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium lenses2013-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
12.85301000.08615.53.8127301127301-375.3
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)
12.852.91000.63723.86384

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1S7C2.8529.91120750120750638999.80.187740.187740.185820.2235RANDOM74.416
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]
-1.56-1.031.440.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.67
r_dihedral_angle_4_deg17.904
r_long_range_B_refined9.968
r_long_range_B_other9.952
r_dihedral_angle_3_deg9.892
r_scangle_other7.667
r_mcangle_it5.884
r_mcangle_other5.884
r_scbond_it5.412
r_scbond_other5.365
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.67
r_dihedral_angle_4_deg17.904
r_long_range_B_refined9.968
r_long_range_B_other9.952
r_dihedral_angle_3_deg9.892
r_scangle_other7.667
r_mcangle_it5.884
r_mcangle_other5.884
r_scbond_it5.412
r_scbond_other5.365
r_mcbond_it3.92
r_mcbond_other3.919
r_dihedral_angle_1_deg2.17
r_angle_refined_deg1.904
r_angle_other_deg1.315
r_chiral_restr0.087
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_gen_planes_other0.011
r_bond_other_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms39992
Nucleic Acid Atoms
Solvent Atoms443
Heterogen Atoms540

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling