8D40 | pdb_00008d40

Crystal structure of human CELSR1 EC1-4

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5V5X	5v5x, 5w4t, 3q2v, 3q2w
experimental model	PDB	5W4T	5v5x, 5w4t, 3q2v, 3q2w
experimental model	PDB	3Q2V	5v5x, 5w4t, 3q2v, 3q2w
experimental model	PDB	3Q2W	5v5x, 5w4t, 3q2v, 3q2w

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	3 M Sodium Chloride, 0.1 M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
6.46	80.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 305.653	α = 90
b = 90.356	β = 96.166
c = 94.949	γ = 90

Symmetry
Space Group	C 1 2 1

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 EIGER X 16M		2020-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9798	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	3.55	47.244	98.7	0.993	10.094	5.7		31176

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.55	3.61	98.2		0.768	2.5	5.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5v5x, 5w4t, 3q2v, 3q2w	3.554	47.244	30766	1483	98.209	0.217	0.2157	0.22	0.2523	0.25	123.797

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]
-14.574		-7.28	14.088		2.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.694
r_dihedral_angle_3_deg	18.291
r_dihedral_angle_4_deg	17.05
r_lrange_it	15.352
r_lrange_other	15.351
r_dihedral_angle_1_deg	9.505
r_scangle_it	9.218
r_scangle_other	9.217
r_mcangle_other	8.273
r_mcangle_it	8.271
r_scbond_it	5.777
r_scbond_other	5.777
r_mcbond_it	5.326
r_mcbond_other	5.317
r_angle_refined_deg	1.932
r_angle_other_deg	1.299
r_metal_ion_refined	0.327
r_nbd_other	0.289
r_nbd_refined	0.272
r_symmetry_nbd_refined	0.22
r_symmetry_nbd_other	0.211
r_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.178
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_refined	0.047
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6647
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	18

Software

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