Experiment: 3MJG

The structure of a platelet derived growth factor receptor complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PDG	PDB entries 1pdg, 1flt
experimental model	PDB	1FLT	PDB entries 1pdg, 1flt

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	0.84 M (NH4)2HPO4, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.47	α = 90
b = 116.82	β = 90
c = 134.15	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	IMAGE PLATE	MAR scanner 300 mm plate		2008-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.9786	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (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	2.3	44.24	98.8	0.078	0.062	14.3	4	55432	54767			36

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.4	97.7		0.327	0.426	3.3	4	8466

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 (Observed)	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 entries 1pdg, 1flt	2.3	44.24	55249	54642	2764	98.9	0.237	0.237	0.2419	0.277	0.2412	RANDOM	67.4

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]
-5.52			11.67		-6.14

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	27.4
c_angle_deg	1.6
c_improper_angle_d	1.19
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5888
Nucleic Acid Atoms
Solvent Atoms	1170
Heterogen Atoms	196

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling