3JUT | pdb_00003jut

Acidic Fibroblast Growth Factor (FGF-1) complexed with gentisic acid

X-RAY DIFFRACTION

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	Equal volumes of protein and inhibitor solutions, 0.75 and 1.5 mM,respectively were mixed with drops containing 60% sodium/potassium tartrate buffered with 5 mM sodium phosphate [pH 7.8]. The drops were equilibrated against 200 ml of 1.3M Li2SO4 and typical crystals grew within two weeks , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.658	α = 90
b = 47.685	β = 106.45
c = 98.413	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	2.21	47.7	98.8	0.082	5.6	3.3	42342	41838			31.73

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	2.21	2.33	94.6		0.328	1.6	3.3	5625

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	2.25	37.01	41838	38199	2034	96.16	0.223	0.21887	0.21587	0.21	0.27406	0.26	RANDOM	38.52

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]
-0.01			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.597
r_dihedral_angle_4_deg	22.66
r_dihedral_angle_3_deg	20.168
r_dihedral_angle_1_deg	8.314
r_scangle_it	3.698
r_scbond_it	2.558
r_angle_refined_deg	2.106
r_mcangle_it	1.62
r_mcbond_it	1.002
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.597
r_dihedral_angle_4_deg	22.66
r_dihedral_angle_3_deg	20.168
r_dihedral_angle_1_deg	8.314
r_scangle_it	3.698
r_scbond_it	2.558
r_angle_refined_deg	2.106
r_mcangle_it	1.62
r_mcbond_it	1.002
r_nbtor_refined	0.311
r_symmetry_hbond_refined	0.264
r_symmetry_vdw_refined	0.252
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.139
r_bond_refined_d	0.026
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6227
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	22

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.