3HO5 | pdb_00003ho5

Crystal structure of Hedgehog-interacting protein (HHIP) and Sonic hedgehog (SHH) complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VHH	PDB entries 1VHH, 3HO4
experimental model	PDB	3HO4	PDB entries 1VHH, 3HO4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	292	0.1 M bis-Tris propane pH 7.0 and 2.2-2.5 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.55	65.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.618	α = 90
b = 101.618	β = 90
c = 302.83	γ = 120

Symmetry
Space Group	P 31 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	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)	2007-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97839	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3	50	99.8	0.085	24.2	8.7	37181	37106		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.11	100		0.589	4.3	8.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB entries 1VHH, 3HO4	3.01	30	35204	35147	1874	99.84	0.23381	0.23381	0.23097	0.2238	0.28738	0.2762	RANDOM	96.674

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]
4.78	2.39		4.78		-7.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.348
r_dihedral_angle_3_deg	19.747
r_dihedral_angle_4_deg	15.728
r_dihedral_angle_1_deg	6.529
r_mcangle_it	3.635
r_scangle_it	3.223
r_mcbond_it	2.161
r_scbond_it	1.997
r_angle_refined_deg	1.186
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.224
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.2
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.08
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8251
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	4

Software

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