5BPB

Crystal structure of the cysteine-rich domain of human Frizzled 4 - Crystal Form I

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IJY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	1.6 M tri-sodium citrate, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.608	α = 90
b = 102.14	β = 90
c = 116.508	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	PIXEL	DECTRIS PILATUS 6M		2013-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.2	41.77	99.2	0.077	12.8	4.3		44268

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27	99.7		0.911	2	4.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1IJY	2.2	40	42000	2227	98.96	0.179	0.1767	0.2227	RANDOM	46.189

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]
-0.33			1.19		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	41.95
r_dihedral_angle_2_deg	34.718
r_dihedral_angle_3_deg	17.597
r_dihedral_angle_4_deg	11.673
r_sphericity_bonded	10.712
r_dihedral_angle_1_deg	6.368
r_mcangle_it	2.903
r_mcbond_it	2.125
r_mcbond_other	2.092
r_rigid_bond_restr	1.523
r_angle_refined_deg	1.279
r_angle_other_deg	0.788
r_chiral_restr	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3866
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	70

Software

Software
Software Name	Purpose
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement