8YYZ | pdb_00008yyz

Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant H-R102A in the absence of metals

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MXW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.2M Ammonium iodide, 20% w/v Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.51	α = 90
b = 84.08	β = 90
c = 126.04	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 PILATUS3 S 2M		2019-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	1.9	42.04	98.4	0.116	0.046	0.99	9.4	7.3		58004

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	1.9	2	91.1		0.53	0.23	0.851	2.7	5.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	THROUGHOUT	1.9	42.04	57921	2422	98.229	0.186	0.1844	0.1927	0.2218	0.2285	27.81

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]
-1.202			2.156		-0.954

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.581
r_dihedral_angle_3_deg	12.229
r_dihedral_angle_2_deg	12.221
r_dihedral_angle_1_deg	7.417
r_lrange_it	5.487
r_lrange_other	5.368
r_scangle_it	2.946
r_scangle_other	2.946
r_mcangle_it	2.279
r_mcangle_other	2.279
r_scbond_it	1.786
r_scbond_other	1.786
r_angle_refined_deg	1.438
r_mcbond_it	1.368
r_mcbond_other	1.368
r_angle_other_deg	0.51
r_nbd_refined	0.203
r_symmetry_nbd_other	0.195
r_xyhbond_nbd_refined	0.192
r_nbtor_refined	0.177
r_nbd_other	0.155
r_symmetry_xyhbond_nbd_refined	0.152
r_symmetry_nbd_refined	0.116
r_symmetry_xyhbond_nbd_other	0.113
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.07
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4483
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing