3BPJ | pdb_00003bpj

Crystal structure of human translation initiation factor 3, subunit 1 alpha

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	291	25% PEG 3350, 0.1M Sodium acetate. Chymotrypsin was added to the crystallization sample at a molar ratio of approx. 1:100, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.902	α = 90
b = 62.373	β = 90
c = 88.056	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	IMAGE PLATE	RIGAKU RAXIS		2007-12-17	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS		2007-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418
2	ROTATING ANODE	RIGAKU FR-E	1.5418

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	1.85	30	99.7	0.041	24.6	7.3		29322

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	1.85	1.92	100		0.877		7.2	2876

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	SIRAS	THROUGHOUT	1.85	25	29151	1442	99.6	0.23	0.229	0.27	0.263	0.3	thin shells (from program SFTOOLS)	39.914

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]
-0.208			-0.654		0.862

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.242
r_dihedral_angle_4_deg	14.822
r_dihedral_angle_3_deg	13.645
r_dihedral_angle_1_deg	5.404
r_scangle_it	3.852
r_mcangle_it	3.214
r_scbond_it	2.774
r_mcbond_it	2.392
r_angle_refined_deg	1.339
r_angle_other_deg	0.947
r_mcbond_other	0.772
r_symmetry_vdw_other	0.369
r_nbd_refined	0.229
r_symmetry_vdw_refined	0.217
r_symmetry_hbond_refined	0.187
r_nbtor_refined	0.18
r_nbd_other	0.168
r_xyhbond_nbd_refined	0.144
r_nbtor_other	0.089
r_chiral_restr	0.085
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2123
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing