5BQC | pdb_00005bqc

Crystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 and sucrose octasulfate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.1 M Tris, pH 8.0, 0.15 M NaCl, 8% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
4.03	69.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.136	α = 90
b = 119.136	β = 90
c = 119.151	γ = 120

Symmetry
Space Group	P 61 2 2

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		2014-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92	Diamond	I04-1

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	3	47.34	100	0.13	0.031	0.999	14.6	19.6		10503

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	3	3.18	100		2.46	0.548	0.149	1.6	20.6	1648

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,5BPU	3	47.34	9904	571	99.92	0.2175	0.2147	0.2629	0.2676	0.2529	RANDOM	113.96

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]
-3	-1.5		-3		9.74

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.748
r_sphericity_bonded	22.406
r_mcangle_it	7.397
r_mcbond_it	5.283
r_mcbond_other	5.28
r_angle_refined_deg	1.181
r_rigid_bond_restr	1.08
r_angle_other_deg	0.935
r_chiral_restr	0.05
r_bond_refined_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.748
r_sphericity_bonded	22.406
r_mcangle_it	7.397
r_mcbond_it	5.283
r_mcbond_other	5.28
r_angle_refined_deg	1.181
r_rigid_bond_restr	1.08
r_angle_other_deg	0.935
r_chiral_restr	0.05
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1759
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	83

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
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.