3K1X | pdb_00003k1x

Acidic Fibroblast Growth Factor (FGF-1) complexed with dobesilate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AXM	PDB ENTRY 1AXM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	295	Crystals of thecomplex between FGF-1 and 2,5-DHPS (2,5-dihydroxyphenylsulfonate) were grown using the sitting drop vapour method at 295 K. Equal volumes of protein and inhibitor solutions, 0.75 and 1.5mM, respectively were mixed with drops containing 60% sodium/potassium tartrate buffered with 5mM sodium phosphate [pH 7.8]. The drops were equilibrated against 0.2ml of 1.3M Li2SO4 and typical crystals grew within two weeks with approximate dimensions of 0.7 x 0.5 x 0.2 mm. , VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.022	α = 90
b = 47.349	β = 106.64
c = 97.975	γ = 90

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 210r		2008-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16	0.979	ESRF	BM16

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	1.98	94.07	98.6	0.05	16	3.7	59910	59016			29.604

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)
	1.98	2.09	92.8		0.342	4.5	3.3	8011

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 ENTRY 1AXM	1.98	24.48	59016	56030	2981	98.5	0.232	0.23041	0.22718	0.23	0.28958	0.29	RANDOM	36.077

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]
0.73		0.61	1.01		-1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.353
r_dihedral_angle_4_deg	19.25
r_dihedral_angle_3_deg	18.798
r_dihedral_angle_1_deg	8.245
r_scangle_it	5.07
r_scbond_it	3.596
r_mcangle_it	2.713
r_angle_refined_deg	2.273
r_mcbond_it	1.669
r_nbtor_refined	0.317
r_symmetry_vdw_refined	0.265
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.187
r_chiral_restr	0.161
r_symmetry_hbond_refined	0.154
r_bond_refined_d	0.026
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6228
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	24

Software

Software
Software Name	Purpose
DNA	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling