5BPQ | pdb_00005bpq

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5BPB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.1 M HEPES, pH 7.5, 0.1 M NaCl, 1.6 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.075	α = 90
b = 76.075	β = 90
c = 204.47	γ = 120

Symmetry
Space Group	P 61

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)	Rpim I (All)	CC (Half)	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	2.4	47.37	99.5	0.046	0.026	0.999	14.5	4		25975

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	99.4		0.606	0.339	0.814	2.2	4.1	2724

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5BPB	2.4	65.88	24639	1322	99.43	0.2058	0.2037	0.24	0.2429	0.23	RANDOM	74.887

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]
0.66	0.33		0.66		-2.15

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	43.226
r_dihedral_angle_2_deg	36.074
r_dihedral_angle_3_deg	19.578
r_dihedral_angle_4_deg	15.154
r_dihedral_angle_1_deg	5.616
r_sphericity_bonded	4.654
r_mcangle_it	1.269
r_angle_refined_deg	1.075
r_mcbond_it	0.972
r_mcbond_other	0.971

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	43.226
r_dihedral_angle_2_deg	36.074
r_dihedral_angle_3_deg	19.578
r_dihedral_angle_4_deg	15.154
r_dihedral_angle_1_deg	5.616
r_sphericity_bonded	4.654
r_mcangle_it	1.269
r_angle_refined_deg	1.075
r_mcbond_it	0.972
r_mcbond_other	0.971
r_angle_other_deg	0.762
r_rigid_bond_restr	0.708
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3765
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.