2Z4U | pdb_00002z4u

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QCG	pdb entry 1qcg

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	298	20% PEG4000, 10% isopropanol, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.12

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm		2006-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.9	EMBL/DESY, HAMBURG	BW7A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.1	30				103537	102812		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.1	1.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1qcg	1.1	10	103537	102812	5	100	0.139	0.122	0.1291	0.146	0.1577	random

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
Key	Refinement Restraint Deviation
s_angle_d	0.03
s_bond_d	0.017
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 Atoms	Number
Protein Atoms	2090
Nucleic Acid Atoms
Solvent Atoms	591
Heterogen Atoms	4

Software

Software
Software Name	Purpose
HKL-2000	data collection
Il	model building
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Il	phasing