4RZ6 | pdb_00004rz6

Transaldolase B E96Q F178Y from E.coli

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ONR	PDB entry 1ONR, monomer

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293.2	0.15M (NH4)2SO4, 18% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.844	α = 90
b = 89.513	β = 90
c = 130.512	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	PIXEL	DECTRIS PILATUS 6M-F		2013-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.072	ESRF	ID29

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	1.8	54.07	98.8	0.09	8.2	4.2	73150	73150

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	1.8	1.9	95.6		0.7	1.6	3.9	10225

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 1ONR, monomer	1.802	54.07	69409	69409	3676	98.61	0.20322	0.20322	0.2008	0.21	0.24907	0.25	RANDOM	31.327

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]
0.52			2.21		-2.73

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	41.633
r_dihedral_angle_2_deg	32.172
r_dihedral_angle_3_deg	14.665
r_sphericity_bonded	12.598
r_dihedral_angle_4_deg	11.177
r_dihedral_angle_1_deg	5.081
r_long_range_B_refined	4.919
r_long_range_B_other	4.919
r_scangle_other	3.951
r_mcangle_it	3.933
r_mcangle_other	3.933
r_scbond_it	3.233
r_scbond_other	3.233
r_mcbond_it	3.103
r_mcbond_other	3.094
r_rigid_bond_restr	2.1
r_angle_refined_deg	1.158
r_angle_other_deg	0.996
r_chiral_restr	0.059
r_bond_refined_d	0.009
r_bond_other_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
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	4946
Nucleic Acid Atoms
Solvent Atoms	365
Heterogen Atoms	43

Software

Software
Software Name	Purpose
MxCuBE	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
Aimless	data scaling