5Z4W | pdb_00005z4w

Crystal structure of signalling protein from buffalo (SPB-40) with an altered conformation of Trp78 at 1.79 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Q7N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	35mM Tris-HCl, 25mM NaCl, 20% ethanol pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.068	α = 90
b = 66.735	β = 90
c = 106.072	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	MARRESEARCH	MIRROR	2013-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.79	56.5	99.6	0.062	2.1	4.2		40939

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.84

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	4Q7N	1.79	56.49	38703	2050	98.6	0.152	0.15	0.16	0.186	0.2	RANDOM	29.43

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]
0.29			-1.2		0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.541
r_dihedral_angle_4_deg	23.177
r_dihedral_angle_3_deg	15.986
r_long_range_B_refined	7.177
r_long_range_B_other	7.171
r_dihedral_angle_1_deg	6.635
r_scangle_other	3.687
r_mcangle_other	2.584
r_mcangle_it	2.582
r_angle_refined_deg	2.529
r_scbond_it	2.38
r_scbond_other	2.379
r_mcbond_it	1.616
r_mcbond_other	1.616
r_angle_other_deg	1.326
r_chiral_restr	0.184
r_bond_refined_d	0.03
r_gen_planes_refined	0.016
r_bond_other_d	0.003
r_gen_planes_other	0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2874
Nucleic Acid Atoms
Solvent Atoms	385
Heterogen Atoms	25

Software

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