4M6R | pdb_00004m6r

Structural and biochemical basis for the inhibition of cell death by APIP, a methionine salvage enzyme


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.42850.04M citric acid, 0.06M bis-tris propane, 5%(v/v) glycerol, 21%(w/v) PEG 3350, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.7455.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.035α = 90
b = 107.735β = 90
c = 192.099γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-10-10MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)1.00000, 0.91977, 0.91957, 0.90633PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1296.05967206922
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0781.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT25068405361695.990.182940.182940.180980.180.220270.22RANDOM30.539
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]
-0.58-1.41.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.744
r_dihedral_angle_3_deg17.153
r_dihedral_angle_4_deg15.788
r_dihedral_angle_1_deg6.555
r_scangle_it4.969
r_scbond_it3.072
r_mcangle_it2.168
r_angle_refined_deg2.049
r_mcbond_it1.216
r_chiral_restr0.21
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7049
Nucleic Acid Atoms
Solvent Atoms567
Heterogen Atoms4

Software

Software
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling