2Z4U

Crystal structure of wild type PD-L4 from Phytolacca dioica leaves


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.529820% PEG4000, 10% isopropanol, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1643.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.521α = 90
b = 58.813β = 90
c = 98.774γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7A0.9EMBL/DESY, HamburgBW7A

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
11.1301035371028121
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.11.2

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1qcg1.11010353710281251000.1390.1220.146random
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]
RMS Deviations
KeyRefinement Restraint Deviation
s_angle_d0.03
s_bond_d0.017
s_similar_dist
s_from_restr_planes
s_zero_chiral_vol
s_non_zero_chiral_vol
s_anti_bump_dis_restr
s_rigid_bond_adp_cmpnt
s_similar_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2090
Nucleic Acid Atoms
Solvent Atoms591
Heterogen Atoms4

Software

Software
Software NamePurpose
HKL-2000data collection
Ilmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
Ilphasing