3D1M | pdb_00003d1m

Crystal Structure of Sonic Hedgehog Bound to the third FNIII domain of CDO

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.3	293	28% PEG 3350, 200 mM MgCl2, 100 mM Tris pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.179	α = 90
b = 98.582	β = 90
c = 144.047	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MAR CCD 165 mm		2007-08-24

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.97893	NSLS	X4C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.7	40	99	0.086	10.3	6.3		55705

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	91.1		0.471		4.5	5054

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 (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	1.7	30.56	55421	2693	99.03	0.189	0.186	0.19	0.229	0.23	RANDOM	33.158

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]
-1.15			-0.87		2.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.59
r_dihedral_angle_4_deg	16.316
r_dihedral_angle_3_deg	13.759
r_dihedral_angle_1_deg	6.428
r_scangle_it	2.985
r_scbond_it	2.031
r_angle_refined_deg	1.416
r_mcangle_it	1.251
r_mcbond_it	0.799
r_nbtor_refined	0.306
r_nbd_refined	0.211
r_symmetry_vdw_refined	0.16
r_symmetry_hbond_refined	0.134
r_xyhbond_nbd_refined	0.111
r_chiral_restr	0.102
r_metal_ion_refined	0.064
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3911
Nucleic Acid Atoms
Solvent Atoms	410
Heterogen Atoms	6

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction