4LHC

Crystal structure of Synechocystis sp. PCC 6803 glycine decarboxylase (P-protein), holo form with pyridoxal-5'-phosphate and glycine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5293100 mM Bicine pH 9, 1.6 M (NH4)3PO4, 5 mM TCEP and 0.2 mM PLP, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthew coefficientSolvent content
2.7455.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.05α = 90
b = 160.05β = 90
c = 159.833γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmultilayer mirror2011-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9334ESRFID14-1

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
11.8999999.90.06818.45.4185699185454
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)
11.8991.9799.10.3714.34.4

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4LGL1.89949.7831.34185699185406931399.890.15620.15460.1856
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]
-1.1334-1.13342.2669
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.916
f_angle_d1.076
f_chiral_restr0.073
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14486
Nucleic Acid Atoms
Solvent Atoms1394
Heterogen Atoms142

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling