2VGG

HUMAN ERYTHROCYTE PYRUVATE KINASE: R479H MUTANT


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.4pH 6.4
Crystal Properties
Matthews coefficientSolvent content
2.5250.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.036α = 90
b = 171.795β = 91.17
c = 85.086γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2001-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7AEMBL/DESY, HAMBURGBW7A

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
12.72092.60.15.52.150701
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)
12.72.890.10.472.11.6

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 2VGB2.74205070075992.60.2540.2530.294RANDOM58.18
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]
0.73-1.04-0.46-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.325
r_dihedral_angle_4_deg22.87
r_dihedral_angle_3_deg21.428
r_dihedral_angle_1_deg5.463
r_scangle_it3.275
r_scbond_it1.966
r_angle_refined_deg1.952
r_mcangle_it1.153
r_mcbond_it0.593
r_symmetry_vdw_refined0.477
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.325
r_dihedral_angle_4_deg22.87
r_dihedral_angle_3_deg21.428
r_dihedral_angle_1_deg5.463
r_scangle_it3.275
r_scbond_it1.966
r_angle_refined_deg1.952
r_mcangle_it1.153
r_mcbond_it0.593
r_symmetry_vdw_refined0.477
r_symmetry_hbond_refined0.373
r_nbtor_refined0.342
r_nbd_refined0.293
r_xyhbond_nbd_refined0.193
r_chiral_restr0.115
r_bond_refined_d0.025
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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 Atoms15181
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing