2VYV

Structure of E.Coli GAPDH Rat Sperm GAPDH heterotetramer


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YVNPDB ENTRY 2YVN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.2M NA FORMATE, 20% PEG 3350, 0.1M HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.142

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.445α = 90
b = 103.562β = 90
c = 177.832γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.1SRSPX10.1

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
12.428.694.50.0710551658
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.382.4378.1

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 2YVN2.3828.6246420243394.60.1840.180.251RANDOM34.9
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]
-0.01-0.030.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.936
r_dihedral_angle_4_deg20.207
r_dihedral_angle_3_deg14.988
r_dihedral_angle_1_deg6.348
r_scangle_it4.384
r_scbond_it3.207
r_mcangle_it2.124
r_mcbond_it1.593
r_angle_refined_deg1.271
r_angle_other_deg0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.936
r_dihedral_angle_4_deg20.207
r_dihedral_angle_3_deg14.988
r_dihedral_angle_1_deg6.348
r_scangle_it4.384
r_scbond_it3.207
r_mcangle_it2.124
r_mcbond_it1.593
r_angle_refined_deg1.271
r_angle_other_deg0.88
r_symmetry_hbond_refined0.21
r_symmetry_vdw_refined0.197
r_nbd_other0.196
r_nbd_refined0.184
r_symmetry_vdw_other0.184
r_xyhbond_nbd_refined0.173
r_nbtor_refined0.171
r_nbtor_other0.085
r_chiral_restr0.069
r_gen_planes_refined0.069
r_bond_refined_d0.01
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms10026
Nucleic Acid Atoms
Solvent Atoms840
Heterogen Atoms228

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing