3HN4

Crystal structure of the NK2 fragment (28-289) of human hepatocyte growth factor/scatter factor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	50 mM Ammonium sulfate, 17-23% PEG 2000 or 4000, 100 mM HEPES pH 8.0, 5% 2-Methyl-2,4-pentanediol, 0.5 mM Beta-octyl glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.15	α = 90
b = 48.15	β = 90
c = 461.673	γ = 120

Symmetry
Space Group	P 65 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	CCD	MARMOSAIC 300 mm CCD		2008-12-17	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2008-12-17	M	SINGLE WAVELENGTH
3	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2009-03-05	M	SINGLE WAVELENGTH
4	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2009-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12700	APS	21-ID-D
2	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12700	APS	21-ID-D
3	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97860	APS	21-ID-G
4	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.07800	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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
1,2,3,4	2.4	50	93.7	0.134	0.134	9.3	6.4	13803	13803

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.44	74.3		0.447	0.447	1.1	2.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1NK1	2.6	41.52	13740	10223	1028	100	0.26952	0.26268	0.33296	RANDOM	37.752

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]
0.18	0.09		0.18		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.406
r_dihedral_angle_3_deg	15.433
r_dihedral_angle_4_deg	13.82
r_dihedral_angle_1_deg	4.58
r_angle_refined_deg	0.867
r_scangle_it	0.542
r_mcangle_it	0.367
r_scbond_it	0.301
r_mcbond_it	0.199
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2089
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	41

Software

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