9M1X | pdb_00009m1x

X-ray structure of human heart fatty acid-binding protein at 0.80 A resolution (holo-FABP3)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4TKJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1M Tris-HCl (pH8.5), 50% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.604	α = 90
b = 69.822	β = 90
c = 33.846	γ = 90

Symmetry
Space Group	P 21 21 21

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	RAYONIX MX300HE		2013-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.800	SPring-8	BL44XU

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	0.8	43.01	99.3	0.113	11.8	9.8		135972

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	0.8	0.81			0.68	2.5

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	0.8	24.31	129053	6847	99.29	0.12747	0.1268	0.1358	0.13993	0.1484	RANDOM	10.124

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]
-0.19			0.14		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_rigid_bond_restr	34.811
r_dihedral_angle_2_deg	34.503
r_sphericity_free	32.619
r_sphericity_bonded	22.242
r_dihedral_angle_4_deg	14.075
r_dihedral_angle_3_deg	12.735
r_long_range_B_refined	7.335
r_long_range_B_other	7.195
r_scbond_it	6.968
r_scbond_other	6.968
r_scangle_other	6.414
r_dihedral_angle_1_deg	6.372
r_mcangle_it	2.141
r_mcangle_other	2.14
r_mcbond_it	2.004
r_mcbond_other	2.002
r_angle_refined_deg	1.982
r_angle_other_deg	0.97
r_chiral_restr	0.096
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1041
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing